diff --git a/CMake/ClangCompilers.cmake b/CMake/ClangCompilers.cmake
index 643c59820..44fb4792e 100644
--- a/CMake/ClangCompilers.cmake
+++ b/CMake/ClangCompilers.cmake
@@ -92,3 +92,12 @@ ENDIF(QMC_BUILD_STATIC)
 SET(CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
 SET(CMAKE_C_FLAGS "$ENV{CC_FLAGS} ${CMAKE_C_FLAGS}")
 
+# Coverage
+IF (ENABLE_GCOV)
+  SET(GCOV_COVERAGE TRUE)
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} --coverage")
+  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
+  SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} --coverage")
+ENDIF(ENABLE_GCOV)
+
diff --git a/CMake/GNUCompilers.cmake b/CMake/GNUCompilers.cmake
index 47399a963..509f65a4d 100755
--- a/CMake/GNUCompilers.cmake
+++ b/CMake/GNUCompilers.cmake
@@ -88,3 +88,13 @@ ENDIF(QMC_BUILD_STATIC)
 SET(CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
 SET(CMAKE_C_FLAGS "$ENV{CC_FLAGS} ${CMAKE_C_FLAGS}")
 
+# Coverage
+IF (ENABLE_GCOV)
+  SET(GCOV_SUPPORTED TRUE)
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} --coverage")
+  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
+  SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} --coverage")
+ENDIF(ENABLE_GCOV)
+
+
diff --git a/CMake/ctest_script.cmake b/CMake/ctest_script.cmake
index 16b684e14..aa3cb1b35 100644
--- a/CMake/ctest_script.cmake
+++ b/CMake/ctest_script.cmake
@@ -118,20 +118,11 @@ ELSEIF( ${CTEST_SCRIPT_ARG} STREQUAL "coverage" )
     SET( CMAKE_BUILD_TYPE "Debug" )
     SET( CTEST_COVERAGE_COMMAND "gcov" )
     SET( ENABLE_GCOV "true" )
-    SET( COVERAGE_OPTIONS
-  "-DCMAKE_CXX_FLAGS=--coverage"
-  "-DCMAKE_C_FLAGS=--coverage"
-  "-DCMAKE_EXE_LINKER_FLAGS=--coverage"
-  "-DCMAKE_SHARED_LINKER_FLAGS=--coverage"
-    )
     SET( CTEST_BUILD_NAME "${CTEST_BUILD_NAME}-coverage" )
 
 ELSE()
     MESSAGE(FATAL_ERROR "Invalid build (${CTEST_SCRIPT_ARG}): ctest -S /path/to/script,build (debug/opt/valgrind")
 ENDIF()
-IF ( NOT COVERAGE_COMMAND )
-    SET( ENABLE_GCOV "false" )
-ENDIF()
 
 
 # Set the number of processors
@@ -244,10 +235,6 @@ IF ( QMC_OPTIONS )
     SET( CTEST_OPTIONS "${CTEST_OPTIONS};${QMC_OPTIONS}" )
 ENDIF()
 
-IF ( COVERAGE_OPTIONS )
-    SET( CTEST_OPTIONS "${CTEST_OPTIONS};${COVERAGE_OPTIONS}" )
-ENDIF()
-
 MESSAGE("Configure options:")
 MESSAGE("   ${CTEST_OPTIONS}")
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4e5c13a2e..d62009e0d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -111,6 +111,10 @@ ELSE(QMC_CUDA)
   MESSAGE("   Full precision = ${OHMMS_PRECISION_FULL}")
 ENDIF(QMC_CUDA)
 
+# Code coverage
+SET(GCOV_SUPPORTED FALSE)
+SET(ENABLE_GCOV FALSE CACHE BOOL "Enable code coverage")
+
 ######################################################################
 # enable MPI and OPNEMP  if possible
 ######################################################################
@@ -495,6 +499,12 @@ ELSE(CMAKE_TOOLCHAIN_FILE)
 
 ENDIF(CMAKE_TOOLCHAIN_FILE)
 
+IF (ENABLE_GCOV)
+  IF (NOT GCOV_SUPPORTED)
+    MESSAGE(FATAL_ERROR "ENABLE_GCOV was specified but compiler does not support GCC coverage flag")
+  ENDIF()
+ENDIF(ENABLE_GCOV)
+
 # check if C++11 is needed by QMCPACK features
 SET(CXX11_NEEDED FALSE)
 IF(BUILD_LMYENGINE_INTERFACE OR BUILD_AFQMC)
diff --git a/tests/coverage/clean_gcda.sh b/tests/coverage/clean_gcda.sh
new file mode 100755
index 000000000..c2365441b
--- /dev/null
+++ b/tests/coverage/clean_gcda.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+find . -name \*.gcda | xargs -i rm {}
diff --git a/tests/coverage/run_coverage.sh b/tests/coverage/run_coverage.sh
new file mode 100755
index 000000000..74d8971db
--- /dev/null
+++ b/tests/coverage/run_coverage.sh
@@ -0,0 +1,104 @@
+#!/bin/bash
+
+# Assumes build has been build with ENABLE_GCOV and DEBUG
+# Run from build directory
+
+# Output:
+#  cov_base - coverage for the base run(s)
+#  cov_unit - coverage for the unit tests (the usual code coverage metric)
+#  cov_diff - coverage for the unit tests relative to the base run
+
+# Each directory contains the *.gcov files, one for each source file.
+# If the 'gcovr' tool is present ( http://gcovr.com/ ), an HTML report is also
+#  produced in cov_detail.html
+
+SRC_ROOT=`pwd`/..
+
+#
+#  Run coverage on the base
+#
+
+echo "Running base coverage"
+
+ctest -L coverage
+
+base_dir="cov_base"
+if [ ! -d $base_dir ]; then
+  mkdir $base_dir
+fi
+
+cd $base_dir
+find `pwd`/.. -name \*.gcda | xargs -i gcov -b -p {}
+
+# Filter out unwanted files
+python ${SRC_ROOT}/tests/coverage/compare_gcov.py -a process --base-dir .
+
+
+# If gcovr is present, create an html report
+if hash gcovr 2>/dev/null; then
+  echo "Generating HTML report for base coverage"
+  # Arguments:
+  # -k - keep the *.gcov files, don't delete them
+  # -g - operation on existing *.gcov files (by default it would run gcov again)
+  # --root - otherwise all the files are filtered out
+  #  Run w/o the --html and --html-details options to get a text summary
+  gcovr -k -g --root=$SRC_ROOT -o cov_detail.html --html --html-details .
+fi
+
+cd ..
+
+${SRC_ROOT}/tests/coverage/clean_gcda.sh
+
+#
+#  Unit test coverage
+#
+
+echo "Running unit test coverage"
+ctest -L unit
+
+unit_dir="cov_unit"
+
+if [ ! -d $unit_dir ]; then
+  mkdir $unit_dir
+fi
+
+cd $unit_dir
+find `pwd`/.. -name \*.gcda | xargs -i gcov -b -p {}
+
+# Filter out unwanted files
+python ${SRC_ROOT}/tests/coverage/compare_gcov.py -a process --base-dir .
+
+# If gcovr is present, create an html report
+if hash gcovr 2>/dev/null; then
+  echo "Creating HTML report for unit tests coverage"
+  gcovr -k -g --root=$SRC_ROOT -o cov_detail.html --html --html-details .
+fi
+
+cd ..
+
+
+#
+# Compute diff
+#
+
+echo "Computing coverage diff"
+
+
+diff_dir="cov_diff"
+
+if [ ! -d $diff_dir ]; then
+  mkdir $diff_dir
+fi
+
+# Compute diff
+python ${SRC_ROOT}/tests/coverage/compare_gcov.py -a compare --base-dir $base_dir --unit-dir $unit_dir --output $diff_dir
+
+cd $diff_dir
+
+# If gcovr is present, create an html report
+if hash gcovr 2>/dev/null; then
+  echo "Creating HTML report for diff coverage"
+  gcovr -k -g --root=$SRC_ROOT -o cov_detail.html --html --html-details .
+fi
+
+cd ..