diff --git a/Source/cmAddCustomCommandCommand.cxx b/Source/cmAddCustomCommandCommand.cxx
index d5f00ff12..6a955506d 100644
--- a/Source/cmAddCustomCommandCommand.cxx
+++ b/Source/cmAddCustomCommandCommand.cxx
@@ -173,6 +173,10 @@ bool cmAddCustomCommandCommand
           break;
         }
 
+      if (cmSystemTools::FileIsFullPath(filename.c_str()))
+        {
+        filename = cmSystemTools::CollapseFullPath(filename);
+        }
        switch (doing)
          {
          case doing_working_directory:
diff --git a/Source/cmCustomCommandGenerator.cxx b/Source/cmCustomCommandGenerator.cxx
index cebd9f5d3..ebfbf7c09 100644
--- a/Source/cmCustomCommandGenerator.cxx
+++ b/Source/cmCustomCommandGenerator.cxx
@@ -103,8 +103,18 @@ std::vector<std::string> const& cmCustomCommandGenerator::GetDepends() const
       {
       cmsys::auto_ptr<cmCompiledGeneratorExpression> cge
                                               = this->GE->Parse(*i);
+      std::vector<std::string> result;
       cmSystemTools::ExpandListArgument(
-                  cge->Evaluate(this->Makefile, this->Config), this->Depends);
+                  cge->Evaluate(this->Makefile, this->Config), result);
+      for (std::vector<std::string>::iterator it = result.begin();
+          it != result.end(); ++it)
+        {
+        if (cmSystemTools::FileIsFullPath(it->c_str()))
+          {
+          *it = cmSystemTools::CollapseFullPath(*it);
+          }
+        }
+      this->Depends.insert(this->Depends.end(), result.begin(), result.end());
       }
     }
   return this->Depends;
diff --git a/Tests/CustomCommand/CMakeLists.txt b/Tests/CustomCommand/CMakeLists.txt
index e0854ceaa..b97cd1642 100644
--- a/Tests/CustomCommand/CMakeLists.txt
+++ b/Tests/CustomCommand/CMakeLists.txt
@@ -456,3 +456,30 @@ add_custom_target(source_in_custom_target SOURCES source_in_custom_target.cpp)
 set_property(SOURCE source_in_custom_target
   PROPERTY COMPILE_DEFINITIONS "TEST"
 )
+
+set(gen_path "${CMAKE_CURRENT_BINARY_DIR}//./foo")
+set(gen_file "${gen_path}/foo.cxx")
+
+add_custom_command(
+  OUTPUT "${gen_file}"
+  # Make sure the output directory exists before trying to write to it.
+  COMMAND ${CMAKE_COMMAND} -E make_directory "${gen_path}"
+  COMMAND ${CMAKE_COMMAND} -E touch "${gen_file}"
+)
+
+add_library(NormOutput "${gen_file}")
+
+set(gen_path "${gen_path}/bar")
+set(gen_file "${gen_path}/bar.cxx")
+
+add_custom_command(
+  OUTPUT "${gen_path}"
+  COMMAND ${CMAKE_COMMAND} -E make_directory "${gen_path}"
+)
+
+add_custom_command(
+  OUTPUT "${gen_file}"
+  DEPENDS "${gen_path}"
+  COMMAND ${CMAKE_COMMAND} -E touch "${gen_file}")
+
+add_library(NormDepends "${gen_file}")