diff --git a/lib/rscons/builder.rb b/lib/rscons/builder.rb
index f715291..a2c27fb 100644
--- a/lib/rscons/builder.rb
+++ b/lib/rscons/builder.rb
@@ -22,12 +22,12 @@ module Rscons
     # Check if the cache is up to date for the target and if not execute the
     # build command.
     # Return the name of the target or false on failure.
-    def standard_build(short_cmd_string, target, command, sources, env, cache)
-      unless cache.up_to_date?(target, command, sources)
+    def standard_build(short_cmd_string, target, command, sources, user_deps, env, cache)
+      unless cache.up_to_date?(target, command, sources, user_deps)
         cache.mkdir_p(File.dirname(target))
         FileUtils.rm_f(target)
         return false unless env.execute(short_cmd_string, command)
-        cache.register_build(target, command, sources)
+        cache.register_build(target, command, sources, user_deps)
       end
       target
     end
diff --git a/lib/rscons/builders/library.rb b/lib/rscons/builders/library.rb
index 8d91370..cefbd3f 100644
--- a/lib/rscons/builders/library.rb
+++ b/lib/rscons/builders/library.rb
@@ -12,7 +12,7 @@ module Rscons
       }
     end
 
-    def run(target, sources, cache, env, vars)
+    def run(target, sources, user_deps, cache, env, vars)
       # build sources to linkable objects
       objects = env.build_sources(sources, [env['OBJSUFFIX'], env['LIBSUFFIX']].flatten, cache, vars)
       if objects
@@ -21,7 +21,7 @@ module Rscons
           '_SOURCES' => objects,
         })
         command = env.build_command(env['ARCMD'], vars)
-        standard_build("AR #{target}", target, command, objects, env, cache)
+        standard_build("AR #{target}", target, command, objects, user_deps, env, cache)
       end
     end
   end
diff --git a/lib/rscons/builders/object.rb b/lib/rscons/builders/object.rb
index c03f3fb..7489dd3 100644
--- a/lib/rscons/builders/object.rb
+++ b/lib/rscons/builders/object.rb
@@ -50,7 +50,7 @@ module Rscons
       end
     end
 
-    def run(target, sources, cache, env, vars)
+    def run(target, sources, user_deps, cache, env, vars)
       vars = vars.merge({
         '_TARGET' => target,
         '_SOURCES' => sources,
@@ -62,7 +62,7 @@ module Rscons
         v.nil? and raise "Error: unknown input file type: #{sources.first.inspect}"
       end.first
       command = env.build_command(env["#{com_prefix}CMD"], vars)
-      unless cache.up_to_date?(target, command, sources)
+      unless cache.up_to_date?(target, command, sources, user_deps)
         cache.mkdir_p(File.dirname(target))
         FileUtils.rm_f(target)
         return false unless env.execute("#{com_prefix} #{target}", command)
@@ -71,7 +71,7 @@ module Rscons
           deps += Environment.parse_makefile_deps(vars['_DEPFILE'], target)
           FileUtils.rm_f(vars['_DEPFILE'])
         end
-        cache.register_build(target, command, deps.uniq)
+        cache.register_build(target, command, deps.uniq, user_deps)
       end
       target
     end
diff --git a/lib/rscons/builders/program.rb b/lib/rscons/builders/program.rb
index 850c80e..1b08de8 100644
--- a/lib/rscons/builders/program.rb
+++ b/lib/rscons/builders/program.rb
@@ -14,7 +14,7 @@ module Rscons
       }
     end
 
-    def run(target, sources, cache, env, vars)
+    def run(target, sources, user_deps, cache, env, vars)
       # build sources to linkable objects
       objects = env.build_sources(sources, [env['OBJSUFFIX'], env['LIBSUFFIX']].flatten, cache, vars)
       return false unless objects
@@ -33,7 +33,7 @@ module Rscons
         'LD' => ld,
       })
       command = env.build_command(env['LDCMD'], vars)
-      standard_build("LD #{target}", target, command, objects, env, cache)
+      standard_build("LD #{target}", target, command, objects, user_deps, env, cache)
     end
   end
 end
diff --git a/lib/rscons/cache.rb b/lib/rscons/cache.rb
index 06133e6..c361ac0 100644
--- a/lib/rscons/cache.rb
+++ b/lib/rscons/cache.rb
@@ -18,9 +18,15 @@ module Rscons
   #           {
   #             'fname' => 'program.o',
   #             'checksum' => '87654321',
-  #           }
+  #           },
   #         ],
-  #       }
+  #         'user_deps' => [
+  #           {
+  #             'fname' => 'lscript.ld',
+  #             'checksum' => '77551133',
+  #           },
+  #         ],
+  #       },
   #       'program.o' => {
   #         'checksum' => '87654321',
   #         'command' => ['gcc', '-c', '-o', 'program.o', 'program.c'],
@@ -32,15 +38,16 @@ module Rscons
   #           {
   #             'fname' => 'program.h',
   #             'checksum' => '7979764643',
-  #           }
-  #         ]
+  #           },
+  #         ],
+  #         'user_deps' => [],
   #       }
-  #     }
+  #     },
   #     directories: {
   #       'build' => true,
   #       'build/one' => true,
   #       'build/two' => true,
-  #     }
+  #     },
   #   }
   class Cache
     #### Constants
@@ -82,6 +89,7 @@ module Rscons
     # @param target [String] The name of the target file.
     # @param command [Array] The command used to build the target.
     # @param deps [Array] List of the target's dependency files.
+    # @param user_deps [Array] List of user-specified extra dependencies.
     # @param options [Hash] Optional options. Can contain the following keys:
     #   :strict_deps::
     #     Only consider a target up to date if its list of dependencies is
@@ -96,7 +104,7 @@ module Rscons
     #     exactly equal to those cached
     #   - each cached dependency file's current checksum matches the checksum
     #     stored in the cache file
-    def up_to_date?(target, command, deps, options = {})
+    def up_to_date?(target, command, deps, user_deps, options = {})
       # target file must exist on disk
       return false unless File.exists?(target)
 
@@ -118,8 +126,11 @@ module Rscons
         return false unless (Set.new(deps) - Set.new(cached_deps)).empty?
       end
 
+      # set of user dependencies must match
+      return false unless user_deps == @cache[:targets][target][:user_deps].map { |dc| dc[:fname] }
+
       # all cached dependencies must have their checksums match
-      @cache[:targets][target][:deps].each do |dep_cache|
+      (@cache[:targets][target][:deps] + @cache[:targets][target][:user_deps]).each do |dep_cache|
         return false unless dep_cache[:checksum] == lookup_checksum(dep_cache[:fname])
       end
 
@@ -130,7 +141,8 @@ module Rscons
     # @param target [String] The name of the target.
     # @param command [Array] The command used to build the target.
     # @param deps [Array] List of dependencies for the target.
-    def register_build(target, command, deps)
+    # @param user_deps [Array] List of user-specified extra dependencies.
+    def register_build(target, command, deps, user_deps)
       @cache[:targets][target.encode(__ENCODING__)] = {
         command: command,
         checksum: calculate_checksum(target),
@@ -139,7 +151,13 @@ module Rscons
             fname: dep.encode(__ENCODING__),
             checksum: lookup_checksum(dep),
           }
-        end
+        end,
+        user_deps: user_deps.map do |dep|
+          {
+            fname: dep.encode(__ENCODING__),
+            checksum: lookup_checksum(dep),
+          }
+        end,
       }
     end
 
diff --git a/lib/rscons/environment.rb b/lib/rscons/environment.rb
index 573d390..ba51fae 100644
--- a/lib/rscons/environment.rb
+++ b/lib/rscons/environment.rb
@@ -147,6 +147,7 @@ module Rscons
           result = run_builder(@targets[target][:builder],
                                target,
                                @targets[target][:source],
+                               [],
                                cache,
                                @targets[target][:vars] || {})
           unless result
@@ -238,7 +239,7 @@ module Rscons
             converted_fname = get_build_fname(source, suffix)
             builder = @builders.values.find { |b| b.produces?(converted_fname, source, self) }
             if builder
-              converted = run_builder(builder, converted_fname, [source], cache, vars)
+              converted = run_builder(builder, converted_fname, [source], [], cache, vars)
               return nil unless converted
               break
             end
@@ -255,18 +256,19 @@ module Rscons
     # @param cache [Cache] The Cache.
     # @param vars [Hash] Extra variables to pass to the builder.
     # Return the result of the builder's run() method.
-    def run_builder(builder, target, sources, cache, vars)
+    def run_builder(builder, target, sources, user_deps, cache, vars)
       vars = @varset.merge(vars)
       @build_hooks.each do |build_hook_block|
         build_operation = {
           builder: builder,
           target: target,
           sources: sources,
+          user_deps: user_deps,
           vars: vars,
         }
         build_hook_block.call(build_operation)
       end
-      builder.run(target, sources, cache, self, vars)
+      builder.run(target, sources, user_deps, cache, self, vars)
     end
 
     # Parse dependencies for a given target from a Makefile.
diff --git a/spec/build_tests_spec.rb b/spec/build_tests_spec.rb
index 78a340d..77c22ec 100644
--- a/spec/build_tests_spec.rb
+++ b/spec/build_tests_spec.rb
@@ -220,7 +220,7 @@ describe Rscons do
   it 'allows Ruby classes as custom builders to be used to construct files' do
    test_dir('custom_builder')
     class MySource < Rscons::Builder
-      def run(target, sources, cache, env, vars = {})
+      def run(target, sources, user_deps, cache, env, vars = {})
         File.open(target, 'w') do |fh|
           fh.puts <<EOF
     #define THE_VALUE 5678
diff --git a/spec/rscons/cache_spec.rb b/spec/rscons/cache_spec.rb
index 1a48061..b995a9a 100644
--- a/spec/rscons/cache_spec.rb
+++ b/spec/rscons/cache_spec.rb
@@ -40,12 +40,12 @@ module Rscons
     describe "#up_to_date?" do
       it "returns false when target file does not exist" do
         File.should_receive(:exists?).with("target").and_return(false)
-        build_from({}).up_to_date?("target", "command", []).should be_false
+        build_from({}).up_to_date?("target", "command", [], []).should be_false
       end
 
       it "returns false when target is not registered in the cache" do
         File.should_receive(:exists?).with("target").and_return(true)
-        build_from({}).up_to_date?("target", "command", []).should be_false
+        build_from({}).up_to_date?("target", "command", [], []).should be_false
       end
 
       it "returns false when the target's checksum does not match" do
@@ -53,7 +53,7 @@ module Rscons
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("def")
-        cache.up_to_date?("target", "command", []).should be_false
+        cache.up_to_date?("target", "command", [], []).should be_false
       end
 
       it "returns false when the build command has changed" do
@@ -61,7 +61,7 @@ module Rscons
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("abc")
-        cache.up_to_date?("target", "command", []).should be_false
+        cache.up_to_date?("target", "command", [], []).should be_false
       end
 
       it "returns false when there is a new dependency" do
@@ -71,7 +71,7 @@ module Rscons
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("abc")
-        cache.up_to_date?("target", "command", ["dep.1", "dep.2"]).should be_false
+        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], []).should be_false
       end
 
       it "returns false when a dependency's checksum has changed" do
@@ -82,13 +82,14 @@ module Rscons
                                                 {fname: "dep.2",
                                                  checksum: "dep.2.chk"},
                                                 {fname: "extra.dep",
-                                                 checksum: "extra.dep.chk"}]}}}
+                                                 checksum: "extra.dep.chk"}],
+                                         user_deps: []}}}
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("abc")
         cache.should_receive(:calculate_checksum).with("dep.1").and_return("dep.1.chk")
         cache.should_receive(:calculate_checksum).with("dep.2").and_return("dep.2.changed")
-        cache.up_to_date?("target", "command", ["dep.1", "dep.2"]).should be_false
+        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], []).should be_false
       end
 
       it "returns false with strict_deps=true when cache has an extra dependency" do
@@ -99,11 +100,44 @@ module Rscons
                                                 {fname: "dep.2",
                                                  checksum: "dep.2.chk"},
                                                 {fname: "extra.dep",
-                                                 checksum: "extra.dep.chk"}]}}}
+                                                 checksum: "extra.dep.chk"}],
+                                         user_deps: []}}}
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("abc")
-        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], strict_deps: true).should be_false
+        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], [], strict_deps: true).should be_false
+      end
+
+      it "returns false when there is a new user dependency" do
+        _cache = {targets: {"target" => {checksum: "abc",
+                                         command: "command",
+                                         deps: [{fname: "dep.1"}],
+                                         user_deps: []}}}
+        cache = build_from(_cache)
+        File.should_receive(:exists?).with("target").and_return(true)
+        cache.should_receive(:calculate_checksum).with("target").and_return("abc")
+        cache.up_to_date?("target", "command", ["dep.1"], ["file.ld"]).should be_false
+      end
+
+      it "returns false when a user dependency checksum has changed" do
+        _cache = {targets: {"target" => {checksum: "abc",
+                                         command: "command",
+                                         deps: [{fname: "dep.1",
+                                                 checksum: "dep.1.chk"},
+                                                {fname: "dep.2",
+                                                 checksum: "dep.2.chk"},
+                                                {fname: "extra.dep",
+                                                 checksum: "extra.dep.chk"}],
+                                         user_deps: [{fname: "user.dep",
+                                                      checksum: "user.dep.chk"}]}}}
+        cache = build_from(_cache)
+        File.should_receive(:exists?).with("target").and_return(true)
+        cache.should_receive(:calculate_checksum).with("target").and_return("abc")
+        cache.should_receive(:calculate_checksum).with("dep.1").and_return("dep.1.chk")
+        cache.should_receive(:calculate_checksum).with("dep.2").and_return("dep.2.chk")
+        cache.should_receive(:calculate_checksum).with("extra.dep").and_return("extra.dep.chk")
+        cache.should_receive(:calculate_checksum).with("user.dep").and_return("INCORRECT")
+        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], ["user.dep"]).should be_false
       end
 
       it "returns true when no condition for false is met" do
@@ -114,14 +148,15 @@ module Rscons
                                                 {fname: "dep.2",
                                                  checksum: "dep.2.chk"},
                                                 {fname: "extra.dep",
-                                                 checksum: "extra.dep.chk"}]}}}
+                                                 checksum: "extra.dep.chk"}],
+                                         user_deps: []}}}
         cache = build_from(_cache)
         File.should_receive(:exists?).with("target").and_return(true)
         cache.should_receive(:calculate_checksum).with("target").and_return("abc")
         cache.should_receive(:calculate_checksum).with("dep.1").and_return("dep.1.chk")
         cache.should_receive(:calculate_checksum).with("dep.2").and_return("dep.2.chk")
         cache.should_receive(:calculate_checksum).with("extra.dep").and_return("extra.dep.chk")
-        cache.up_to_date?("target", "command", ["dep.1", "dep.2"]).should be_true
+        cache.up_to_date?("target", "command", ["dep.1", "dep.2"], []).should be_true
       end
     end
 
@@ -132,7 +167,8 @@ module Rscons
         cache.should_receive(:calculate_checksum).with("the target").and_return("the checksum")
         cache.should_receive(:calculate_checksum).with("dep 1").and_return("dep 1 checksum")
         cache.should_receive(:calculate_checksum).with("dep 2").and_return("dep 2 checksum")
-        cache.register_build("the target", "the command", ["dep 1", "dep 2"])
+        cache.should_receive(:calculate_checksum).with("user.dep").and_return("user.dep checksum")
+        cache.register_build("the target", "the command", ["dep 1", "dep 2"], ["user.dep"])
         cached_target = cache.instance_variable_get(:@cache)[:targets]["the target"]
         cached_target.should_not be_nil
         cached_target[:command].should == "the command"
@@ -141,6 +177,9 @@ module Rscons
           {fname: "dep 1", checksum: "dep 1 checksum"},
           {fname: "dep 2", checksum: "dep 2 checksum"},
         ]
+        cached_target[:user_deps].should == [
+          {fname: "user.dep", checksum: "user.dep checksum"},
+        ]
       end
     end
 
diff --git a/spec/rscons/environment_spec.rb b/spec/rscons/environment_spec.rb
index 52b94a5..9aa4131 100644
--- a/spec/rscons/environment_spec.rb
+++ b/spec/rscons/environment_spec.rb
@@ -114,7 +114,7 @@ module Rscons
 
         cache = "cache"
         Cache.should_receive(:new).and_return(cache)
-        env.should_receive(:run_builder).with(anything, "a.out", ["main.c"], cache, {}).and_return(true)
+        env.should_receive(:run_builder).with(anything, "a.out", ["main.c"], [], cache, {}).and_return(true)
         cache.should_receive(:write)
 
         env.process
@@ -127,8 +127,8 @@ module Rscons
 
         cache = "cache"
         Cache.should_receive(:new).and_return(cache)
-        env.should_receive(:run_builder).with(anything, "main.o", ["other.cc"], cache, {}).and_return("main.o")
-        env.should_receive(:run_builder).with(anything, "a.out", ["main.o"], cache, {}).and_return("a.out")
+        env.should_receive(:run_builder).with(anything, "main.o", ["other.cc"], [], cache, {}).and_return("main.o")
+        env.should_receive(:run_builder).with(anything, "a.out", ["main.o"], [], cache, {}).and_return("a.out")
         cache.should_receive(:write)
 
         env.process
@@ -141,7 +141,7 @@ module Rscons
 
         cache = "cache"
         Cache.should_receive(:new).and_return(cache)
-        env.should_receive(:run_builder).with(anything, "main.o", ["other.cc"], cache, {}).and_return(false)
+        env.should_receive(:run_builder).with(anything, "main.o", ["other.cc"], [], cache, {}).and_return(false)
         cache.should_receive(:write)
 
         expect { env.process }.to raise_error BuildError, /Failed.to.build.main.o/
@@ -241,8 +241,8 @@ module Rscons
         cache = "cache"
         env = Environment.new
         env.add_builder(ABuilder.new)
-        env.builders["Object"].should_receive(:run).with("mod.o", ["mod.c"], cache, env, anything).and_return("mod.o")
-        env.builders["ABuilder"].should_receive(:run).with("mod2.ab_out", ["mod2.ab_in"], cache, env, anything).and_return("mod2.ab_out")
+        env.builders["Object"].should_receive(:run).with("mod.o", ["mod.c"], [], cache, env, anything).and_return("mod.o")
+        env.builders["ABuilder"].should_receive(:run).with("mod2.ab_out", ["mod2.ab_in"], [], cache, env, anything).and_return("mod2.ab_out")
         env.build_sources(["precompiled.o", "mod.c", "mod2.ab_in"], [".o", ".ab_out"], cache, {}).should == ["precompiled.o", "mod.o", "mod2.ab_out"]
       end
     end
@@ -255,14 +255,14 @@ module Rscons
             build_op[:vars]["CFLAGS"] += ["-O3", "-DSPECIAL"]
           end
         end
-        env.builders["Object"].stub(:run) do |target, sources, cache, env, vars|
+        env.builders["Object"].stub(:run) do |target, sources, user_deps, cache, env, vars|
           vars["CFLAGS"].should == []
         end
-        env.run_builder(env.builders["Object"], "build/normal/module.o", ["src/normal/module.c"], "cache", {})
-        env.builders["Object"].stub(:run) do |target, sources, cache, env, vars|
+        env.run_builder(env.builders["Object"], "build/normal/module.o", ["src/normal/module.c"], [], "cache", {})
+        env.builders["Object"].stub(:run) do |target, sources, user_deps, cache, env, vars|
           vars["CFLAGS"].should == ["-O3", "-DSPECIAL"]
         end
-        env.run_builder(env.builders["Object"], "build/special/module.o", ["src/special/module.c"], "cache", {})
+        env.run_builder(env.builders["Object"], "build/special/module.o", ["src/special/module.c"], [], "cache", {})
       end
     end