diff --git a/Modules/FindCUDA.cmake b/Modules/FindCUDA.cmake
index aad4f21e0..1de9042cf 100644
--- a/Modules/FindCUDA.cmake
+++ b/Modules/FindCUDA.cmake
@@ -813,6 +813,43 @@ function(CUDA_BUILD_SHARED_LIBRARY shared_flag)
   set(${shared_flag} ${_cuda_build_shared_libs} PARENT_SCOPE)
 endfunction()
 
+##############################################################################
+# Helper to avoid clashes of files with the same basename but different paths.
+# This doesn't attempt to do exactly what CMake internals do, which is to only
+# add this path when there is a conflict, since by the time a second collision
+# in names is detected it's already too late to fix the first one.  For
+# consistency sake the relative path will be added to all files.
+function(CUDA_COMPUTE_BUILD_PATH path build_path)
+  #message("CUDA_COMPUTE_BUILD_PATH([${path}] ${build_path})")
+  # Only deal with CMake style paths from here on out
+  file(TO_CMAKE_PATH "${path}" bpath)
+  if (IS_ABSOLUTE "${bpath}")
+    # Absolute paths are generally unnessary, especially if something like
+    # FILE(GLOB_RECURSE) is used to pick up the files.
+    file(RELATIVE_PATH bpath "${CMAKE_CURRENT_SOURCE_DIR}" "${bpath}")
+  endif()
+
+  # This recipie is from cmLocalGenerator::CreateSafeUniqueObjectFileName in the
+  # CMake source.
+
+  # Remove leading /
+  string(REGEX REPLACE "^[/]+" "" bpath "${bpath}")
+  # Avoid absolute paths by removing ':'
+  string(REPLACE ":" "_" bpath "${bpath}")
+  # Avoid relative paths that go up the tree
+  string(REPLACE "../" "__/" bpath "${bpath}")
+  # Avoid spaces
+  string(REPLACE " " "_" bpath "${bpath}")
+
+  # Strip off the filename.  I wait until here to do it, since removin the
+  # basename can make a path that looked like path/../basename turn into
+  # path/.. (notice the trailing slash).
+  get_filename_component(bpath "${bpath}" PATH)
+
+  set(${build_path} "${bpath}" PARENT_SCOPE)
+  #message("${build_path} = ${bpath}")
+endfunction()
+
 ##############################################################################
 # This helper macro populates the following variables and setups up custom
 # commands and targets to invoke the nvcc compiler to generate C or PTX source
@@ -982,13 +1019,6 @@ macro(CUDA_WRAP_SRCS cuda_target format generated_files)
     list(APPEND nvcc_flags "-D${cuda_target}_EXPORTS")
   endif()
 
-  # Determine output directory
-  if(CUDA_GENERATED_OUTPUT_DIR)
-    set(cuda_compile_output_dir "${CUDA_GENERATED_OUTPUT_DIR}")
-  else()
-    set(cuda_compile_output_dir "${CMAKE_CURRENT_BINARY_DIR}")
-  endif()
-
   # Reset the output variable
   set(_cuda_wrap_generated_files "")
 
@@ -999,6 +1029,19 @@ macro(CUDA_WRAP_SRCS cuda_target format generated_files)
     get_source_file_property(_is_header ${file} HEADER_FILE_ONLY)
     if(${file} MATCHES ".*\\.cu$" AND NOT _is_header)
 
+      # Determine output directory
+      cuda_compute_build_path("${file}" cuda_build_path)
+      set(cuda_compile_intermediate_directory "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${cuda_target}.dir/${cuda_build_path}")
+      if(CUDA_GENERATED_OUTPUT_DIR)
+        set(cuda_compile_output_dir "${CUDA_GENERATED_OUTPUT_DIR}")
+      else()
+        if ( compile_to_ptx )
+          set(cuda_compile_output_dir "${CMAKE_CURRENT_BINARY_DIR}")
+        else()
+          set(cuda_compile_output_dir "${cuda_compile_intermediate_directory}")
+        endif()
+      endif()
+
       # Add a custom target to generate a c or ptx file. ######################
 
       get_filename_component( basename ${file} NAME )
@@ -1018,10 +1061,10 @@ macro(CUDA_WRAP_SRCS cuda_target format generated_files)
       # argument, so that the ${CMAKE_CFG_INTDIR} gets expanded at run time
       # instead of configure time.
       set(generated_file "${generated_file_path}/${generated_file_basename}")
-      set(cmake_dependency_file "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${generated_file_basename}.depend")
-      set(NVCC_generated_dependency_file "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${generated_file_basename}.NVCC-depend")
+      set(cmake_dependency_file "${cuda_compile_intermediate_directory}/${generated_file_basename}.depend")
+      set(NVCC_generated_dependency_file "${cuda_compile_intermediate_directory}/${generated_file_basename}.NVCC-depend")
       set(generated_cubin_file "${generated_file_path}/${generated_file_basename}.cubin.txt")
-      set(custom_target_script "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${generated_file_basename}.cmake")
+      set(custom_target_script "${cuda_compile_intermediate_directory}/${generated_file_basename}.cmake")
 
       # Setup properties for obj files:
       if( NOT compile_to_ptx )
@@ -1101,6 +1144,7 @@ macro(CUDA_WRAP_SRCS cuda_target format generated_files)
           -D "generated_file:STRING=${generated_file}"
           -D "generated_cubin_file:STRING=${generated_cubin_file}"
           -P "${custom_target_script}"
+        WORKING_DIRECTORY "${cuda_compile_intermediate_directory}"
         COMMENT "${cuda_build_comment_string}"
         )