diff --git a/CMakeLists.txt b/CMakeLists.txt
index 882d7bf74..486888c8b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,6 +32,7 @@ option(RDK_BUILD_SWIG_CSHARP_WRAPPER "build the experimental SWIG C# wrappers (d
 option(RDK_TEST_MMFF_COMPLIANCE "run MMFF compliance tests (requires tar/gzip)" ON )
 option(RDK_BUILD_CPP_TESTS "build the c++ tests (disabing can speed up builds" ON)
 option(RDK_USE_FLEXBISON "use flex/bison, if available, to build the SMILES/SMARTS/SLN parsers" OFF)
+option(RDK_TEST_COVERAGE "Use G(L)COV to compute test coverage" OFF)
 
 if(RDK_BUILD_SWIG_WRAPPERS!=ON)
   set(RDK_BUILD_SWIG_JAVA_WRAPPER OFF)
@@ -194,12 +195,36 @@ endif()
 
 
 # setup our compiler flags:
-if(CMAKE_COMPILER_IS_GNUCXX)
-  ADD_DEFINITIONS("-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC")
-endif()
-if(CMAKE_COMPILER_IS_CLANG)
-  ADD_DEFINITIONS("-Wno-array-bounds -fPIC")
-endif()
+if (RDK_TEST_COVERAGE)
+ if (NOT RDK_USE_FLEXBISON)
+   message(FATAL_ERROR, "Test coverage doesn't current work unless FLEX and BISON are run.")
+ endif(NOT RDK_USE_FLEXBISON)
+
+ message("====== Installing test coverage support ======")
+ message("  To run:")
+ message("   make install")
+ message("   make RDKit_coverage")
+ message("")
+ message(" open <build_dir>/coverage/index.html")
+ message("")
+ message(" If any of the RDKit tests fail, coverage will probably not be generated.")
+ message("====== Installing test coverage support ======")
+ message("")
+ 
+ INCLUDE(CodeCoverage)
+ SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+ SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+ message("== setup_target_for_coverage(${PROJECT_NAME}_coverage test coverage)")
+ setup_target_for_coverage(${PROJECT_NAME}_coverage ctest coverage)
+
+else(RDK_TEST_COVERAGE)
+ if(CMAKE_COMPILER_IS_GNUCXX)
+   ADD_DEFINITIONS("-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC")
+ endif()
+ if(CMAKE_COMPILER_IS_CLANG)
+   ADD_DEFINITIONS("-Wno-array-bounds -fPIC")
+ endif()
+endif(RDK_TEST_COVERAGE)
 
 if(NOT RDK_INSTALL_INTREE)
   install(DIRECTORY Data DESTINATION
@@ -287,6 +312,7 @@ SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CMake ${CMake_VERSION_MAJOR}.${CMake_VERSIO
 #ENDIF(WIN32 AND NOT UNIX)
 #SET(CPACK_PACKAGE_EXECUTABLES "MyExecutable" "My Executable")
 
+
 SET(CPACK_SET_DESTDIR ON)
 
 INCLUDE(CPack)
diff --git a/Code/cmake/Modules/CodeCoverage.cmake b/Code/cmake/Modules/CodeCoverage.cmake
new file mode 100644
index 000000000..9feb281c3
--- /dev/null
+++ b/Code/cmake/Modules/CodeCoverage.cmake
@@ -0,0 +1,170 @@
+#
+# 2012-01-31, Lars Bilke
+# - Enable Code Coverage
+#
+# 2013-09-17, Joakim Söderberg
+# - Added support for Clang.
+# - Some additional usage instructions.
+#
+# 2015-01-14, Brian Kelley
+# - Fix FLEX and BISON coverage (ignore certain files)
+#
+# USAGE:
+
+# 0. (Mac only) If you use Xcode 5.1 make sure to patch geninfo as described here:
+#      http://stackoverflow.com/a/22404544/80480
+#
+# 1. Copy this file into your cmake modules path.
+#
+# 2. Add the following line to your CMakeLists.txt:
+#      INCLUDE(CodeCoverage)
+#
+# 3. Set compiler flags to turn off optimization and enable coverage: 
+#    SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+#	 SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
+#  
+# 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target
+#    which runs your test executable and produces a lcov code coverage report:
+#    Example:
+#	 SETUP_TARGET_FOR_COVERAGE(
+#				my_coverage_target  # Name for custom target.
+#				test_driver         # Name of the test driver executable that runs the tests.
+#									# NOTE! This should always have a ZERO as exit code
+#									# otherwise the coverage generation will not complete.
+#				coverage            # Name of output directory.
+#				)
+#
+# 4. Build a Debug build:
+#	 cmake -DCMAKE_BUILD_TYPE=Debug ..
+#	 make
+#	 make my_coverage_target
+#
+#
+
+# Check prereqs
+FIND_PROGRAM( GCOV_PATH gcov )
+FIND_PROGRAM( LCOV_PATH lcov )
+FIND_PROGRAM( GENHTML_PATH genhtml )
+FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests)
+
+IF(NOT GCOV_PATH)
+	MESSAGE(FATAL_ERROR "gcov not found! Aborting...")
+ENDIF() # NOT GCOV_PATH
+
+IF(NOT CMAKE_COMPILER_IS_GNUCXX)
+	# Clang version 3.0.0 and greater now supports gcov as well.
+	MESSAGE(WARNING "Compiler is not GNU gcc! Clang Version 3.0.0 and greater supports gcov as well, but older versions don't.")
+	
+	IF(NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+		MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
+	ENDIF()
+ENDIF() # NOT CMAKE_COMPILER_IS_GNUCXX
+
+SET(CMAKE_CXX_FLAGS_COVERAGE
+    "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+    CACHE STRING "Flags used by the C++ compiler during coverage builds."
+    FORCE )
+SET(CMAKE_C_FLAGS_COVERAGE
+    "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+    CACHE STRING "Flags used by the C compiler during coverage builds."
+    FORCE )
+SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used for linking binaries during coverage builds."
+    FORCE )
+SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used by the shared libraries linker during coverage builds."
+    FORCE )
+MARK_AS_ADVANCED(
+    CMAKE_CXX_FLAGS_COVERAGE
+    CMAKE_C_FLAGS_COVERAGE
+    CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
+
+IF ( NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "Coverage"))
+  MESSAGE( WARNING "Code coverage results with an optimized (non-Debug) build may be misleading" )
+ENDIF() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
+
+
+# Param _targetname     The name of new the custom make target
+# Param _testrunner     The name of the target which runs the tests.
+#						MUST return ZERO always, even on errors. 
+#						If not, no coverage report will be created!
+# Param _outputname     lcov output is generated as _outputname.info
+#                       HTML report is generated in _outputname/index.html
+# Optional fourth parameter is passed as arguments to _testrunner
+#   Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname)
+
+	IF(NOT LCOV_PATH)
+		MESSAGE(FATAL_ERROR "lcov not found! Aborting...")
+	ENDIF() # NOT LCOV_PATH
+
+	IF(NOT GENHTML_PATH)
+		MESSAGE(FATAL_ERROR "genhtml not found! Aborting...")
+	ENDIF() # NOT GENHTML_PATH
+
+	SET(IN_TREE_FILE_FIXUP "${CMAKE_SOURCE_DIR}/CMakeModules/in_tree_file_fixup.py")
+
+	# Setup target
+	ADD_CUSTOM_TARGET(${_targetname}
+		
+		# Cleanup lcov
+		${LCOV_PATH} --directory . --zerocounters
+		
+		# Run tests
+		COMMAND ${_testrunner} ${ARGV3}
+		# Capturing lcov counters and generating report
+		COMMAND ${LCOV_PATH} --directory . --capture --output-file ${_outputname}.info
+		COMMAND ${LCOV_PATH} --remove ${_outputname}.info 'tests/*' '/usr/*' '*.ll' '*.yy' --output-file ${_outputname}.info.cleaned
+                COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/Code/cmake/Modules/fixup_coverage.py ${CMAKE_SOURCE_DIR} ${_outputname}.info.cleaned
+
+		COMMAND ${GENHTML_PATH} -o ${_outputname} ${_outputname}.info.cleaned
+		COMMAND ${CMAKE_COMMAND} -E remove ${_outputname}.info ${_outputname}.info.cleaned
+		
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+		COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+	)
+
+	# Show info where to find the report
+	ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+		COMMAND ;
+		COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report."
+	)
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
+
+# Param _targetname     The name of new the custom make target
+# Param _testrunner     The name of the target which runs the tests
+# Param _outputname     cobertura output is generated as _outputname.xml
+# Optional fourth parameter is passed as arguments to _testrunner
+#   Pass them in list form, e.g.: "-j;2" for -j 2
+FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
+
+	IF(NOT PYTHON_EXECUTABLE)
+		MESSAGE(FATAL_ERROR "Python not found! Aborting...")
+	ENDIF() # NOT PYTHON_EXECUTABLE
+
+	IF(NOT GCOVR_PATH)
+		MESSAGE(FATAL_ERROR "gcovr not found! Aborting...")
+	ENDIF() # NOT GCOVR_PATH
+
+	ADD_CUSTOM_TARGET(${_targetname}
+
+		# Run tests
+		${_testrunner} ${ARGV3}
+
+		# Running gcovr
+		COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/'  -o ${_outputname}.xml
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+		COMMENT "Running gcovr to produce Cobertura code coverage report."
+	)
+
+	# Show info where to find the report
+	ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
+		COMMAND ;
+		COMMENT "Cobertura code coverage report saved in ${_outputname}.xml."
+	)
+
+ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA
\ No newline at end of file
diff --git a/Code/cmake/Modules/fixup_coverage.py b/Code/cmake/Modules/fixup_coverage.py
new file mode 100644
index 000000000..e280c818b
--- /dev/null
+++ b/Code/cmake/Modules/fixup_coverage.py
@@ -0,0 +1,34 @@
+"""This file searches the source directory for BISON and FLEX files that
+the coverage tool mistakenly finds in the build tree.
+It replaces the paths with the ones from the source tree
+n.b. if a file with the same name (i.e. sln.yy) is found twice
+ in the source tree, this will break"""
+
+import os,sys
+source_dir, info_file = sys.argv[1:3]
+print source_dir, info_file
+
+paths = {}
+for root, dir, files in os.walk(source_dir):
+    for f in files:
+        paths[f] = paths.get(f, []) + [os.path.join(root, f)]
+
+lines = open(info_file).readlines()
+
+newlines = []
+for line in lines:
+    if "SF:" in line:
+        fn = line.split("SF:")[-1].strip()
+        if not os.path.exists(fn):
+            print "Does not exist:", fn.strip()
+            head, rest = os.path.split(fn)
+            potential = paths[rest]
+            if len(potential) == 1:
+                line = "SF:"+potential[0]
+            else:
+                asdf
+    newlines.append(line)
+
+open(info_file, 'w').write("\n".join(newlines))
+                
+