diff --git a/lib/gcovinator.rb b/lib/gcovinator.rb
index 408851b..00fdb19 100644
--- a/lib/gcovinator.rb
+++ b/lib/gcovinator.rb
@@ -12,7 +12,7 @@ module Gcovinator
 
   class << self
 
-    def run(build_dir, source_dirs, files, output_dir)
+    def run(build_dir, source_dirs, files, output_dir, prefix)
       build_dir = Pathname.new(File.expand_path(build_dir)).cleanpath.to_s
       source_dirs = ["."] if source_dirs.empty?
       source_dirs = source_dirs.map do |s|
@@ -23,6 +23,7 @@ module Gcovinator
         Pathname.new(File.expand_path(f)).cleanpath.to_s
       end
       output_dir = Pathname.new(File.expand_path(output_dir)).cleanpath.to_s
+      prefix = Pathname.new(File.expand_path(prefix)).cleanpath.to_s
       file_coverages = {}
       Dir.mktmpdir do |dir|
         Dir.chdir(dir) do
@@ -38,7 +39,7 @@ module Gcovinator
       end
       FileUtils.mkdir_p(output_dir)
       file_reports = file_coverages.each_with_index.map do |(source_file_name, file_coverage), i|
-        FileReport.new(source_file_name, file_coverage, source_dirs, output_dir, sprintf("s%04d.html", i))
+        FileReport.new(source_file_name, file_coverage, prefix, output_dir, sprintf("s%04d.html", i))
       end
       IndexReport.new(output_dir, file_reports)
     end
diff --git a/lib/gcovinator/cli.rb b/lib/gcovinator/cli.rb
index b1a530c..89b34f2 100644
--- a/lib/gcovinator/cli.rb
+++ b/lib/gcovinator/cli.rb
@@ -11,6 +11,7 @@ module Gcovinator
         build_dir = "."
         source_dirs = []
         output_dir = "coverage"
+        prefix = "."
 
         OptionParser.new do |opts|
 
@@ -35,6 +36,10 @@ module Gcovinator
             output_dir = o
           end
 
+          opts.on("-p PREFIX", "--prefix PREFIX", "Prefix path to strip from source file paths. Defaults to '.' if not specified.") do |p|
+            prefix = p
+          end
+
           opts.on("-s SRCDIR", "--source-dir SRCDIR", "Specify a source directory. Reports will only be generated for sources under a specified source directory. Multiple source directories may be specified. Defaults to '.' if not specified.") do |s|
             source_dirs << s
           end
@@ -46,7 +51,7 @@ module Gcovinator
 
         end.parse!(argv)
 
-        Gcovinator.run(build_dir, source_dirs, argv, output_dir)
+        Gcovinator.run(build_dir, source_dirs, argv, output_dir, prefix)
       end
 
     end
diff --git a/lib/gcovinator/file_report.rb b/lib/gcovinator/file_report.rb
index 1a14571..37475d6 100644
--- a/lib/gcovinator/file_report.rb
+++ b/lib/gcovinator/file_report.rb
@@ -8,8 +8,8 @@ module Gcovinator
     attr_reader :source_file_name
     attr_reader :report_file_name
 
-    def initialize(source_file_name, file_coverage, source_dirs, output_dir, report_file_name)
-      @source_file_name = clean_source_file_name(source_file_name, source_dirs)
+    def initialize(source_file_name, file_coverage, prefix, output_dir, report_file_name)
+      @source_file_name = clean_source_file_name(source_file_name, prefix)
       @report_file_name = report_file_name
       @total_lines = 0
       @covered_lines = 0
@@ -20,12 +20,10 @@ module Gcovinator
 
     private
 
-    def clean_source_file_name(source_file_name, source_dirs)
-      source_dirs.each do |source_dir|
-        prefix_test = "#{source_dir}/"
-        if source_file_name.start_with?(prefix_test)
-          return source_file_name[prefix_test.size, source_file_name.size]
-        end
+    def clean_source_file_name(source_file_name, prefix)
+      prefix_test = "#{prefix}/"
+      if source_file_name.start_with?(prefix_test)
+        return source_file_name[prefix_test.size, source_file_name.size]
       end
       source_file_name
     end