diff --git a/.gitignore b/.gitignore
index b664c409bf7..da8415ae292 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,6 +27,7 @@
 *.o-*
 *.exe
 *.a
+*.gch
 
 # /doc/
 /doc/api
diff --git a/make/tests b/make/tests
index 1828daa5362..a324a1ba53c 100644
--- a/make/tests
+++ b/make/tests
@@ -9,20 +9,16 @@ GTEST_CXXFLAGS += -isystem $(GTEST)/include -isystem $(GTEST) -O$O
 ##
 # Build the google test library.
 ##
-$(GTEST)/src/gtest-all.o: CXXFLAGS += $(GTEST_CXXFLAGS)
-
-test/%$(EXE) : CXXFLAGS += $(GTEST_CXXFLAGS)
-test/%$(EXE) : test/%.o $(GTEST_MAIN) $(GTEST)/src/gtest-all.o
-	$(LINK.cpp) -o $@ $^
-
-
+$(GTEST)/src/gtest-all.o: $(GTEST)/src/gtest-all.cc
+	$(COMPILE.cpp) -o $@ $<
 
+$(GTEST)/%.cc: ;
 
 ##
 # Rule for generating dependencies.
 ##
-.PRECIOUS: test/%.d
-test/%.d : test/%.cpp
+.PRECIOUS: %.d
+%.d : %.cpp
 	@mkdir -p $(dir $@)
 	@set -e; \
 	rm -f $@; \
@@ -30,6 +26,15 @@ test/%.d : test/%.cpp
 	sed -e 's,\($(*F)\)\.o[ :]*,$(@D)/\1.o $@ : ,g' < $@.$$$$ > $@; \
 	rm -f $@.$$$$
 
+%.d : %.hpp
+	@mkdir -p $(dir $@)
+	@set -e; \
+	rm -f $@; \
+	$(COMPILE.cpp) -MM $< > $@.$$$$; \
+	sed -e 's,\($(*F)\)\.o[ :]*,$(@D)/\1.hpp.gch $@ : ,g' < $@.$$$$ > $@; \
+	rm -f $@.$$$$
+    $(eval include $$@)
+
 ##
 # Adding a test for multiple translation units. If this fails,
 # a new function is probably missing an inline
@@ -43,6 +48,7 @@ test/unit/libmultiple.so : test/unit/multiple_translation_units1.o test/unit/mul
 
 test/unit/multiple_translation_units_test.cpp : test/unit/libmultiple.so
 
+
 ############################################################
 #
 # CVODES tests
@@ -76,6 +82,89 @@ test/dummy.cpp:
 .PHONY: test-headers
 test-headers: $(HEADER_TESTS)
 
+test/unit/math_include_test.o: test/unit/math_include_test.cpp
+	$(COMPILE.cpp) $< -o $@
+
+############################################################
+#
+# General make targets for tests
+# (necessary now that implicit SUFFIX rules are actually turned off)
+#
+
+test/%$(EXE) : CXXFLAGS += $(GTEST_CXXFLAGS)
+test/%$(EXE) : test/%.o $(GTEST_MAIN) $(GTEST)/src/gtest-all.o
+	$(LINK.cpp) -o $@ $^
+
+# We need these explicit targets here because we turned off suffixes. We can't
+# make a more general pattern rule like test/%.o because we want to force make
+# to generate the pre-compiled headers (below) when applicable.
+test/unit/math_c11_test.o: test/unit/math_c11_test.cpp
+	$(COMPILE.cpp) $< -o $@
+
+test/unit/math/memory/%.o: test/unit/math/memory/%.cpp
+	$(COMPILE.cpp) $< -o $@
+
+############################################################
+#
+# Targets to include proper pre-compiled header files (.hpp.gch) for unit tests
+# and distribution tests 
+##
+
+.PRECIOUS: %.hpp.gch test/%.o
+
+%.hpp.gch: %.hpp %.d
+	$(COMPILE.cpp) -o $@ $(@:.gch=)
+
+test/prob/%.o : stan/math/mix/mat.hpp.gch test/prob/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/prim/scal/%.o : stan/math/prim/scal.hpp.gch test/unit/math/prim/scal/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/prim/arr/%.o : stan/math/prim/arr.hpp.gch test/unit/math/prim/arr/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/prim/mat/%.o : stan/math/prim/mat.hpp.gch test/unit/math/prim/mat/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/rev/core/%.o : stan/math/rev/core.hpp.gch test/unit/math/rev/core/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/rev/scal/%.o : stan/math/rev/scal.hpp.gch test/unit/math/rev/scal/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/rev/arr/%.o : stan/math/rev/arr.hpp.gch test/unit/math/rev/arr/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/rev/mat/%.o : stan/math/rev/mat.hpp.gch test/unit/math/rev/mat/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/fwd/core/%.o : stan/math/fwd/core.hpp.gch test/unit/math/fwd/core/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/fwd/scal/%.o : stan/math/fwd/scal.hpp.gch test/unit/math/fwd/scal/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/fwd/arr/%.o : stan/math/fwd/arr.hpp.gch test/unit/math/fwd/arr/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/fwd/mat/%.o : stan/math/fwd/mat.hpp.gch test/unit/math/fwd/mat/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/mix/scal/%.o : stan/math/mix/scal.hpp.gch test/unit/math/mix/scal/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/mix/arr/%.o : stan/math/mix/arr.hpp.gch test/unit/math/mix/arr/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+test/unit/math/mix/mat/%.o : stan/math/mix/mat.hpp.gch test/unit/math/mix/mat/%.cpp
+	$(COMPILE.cpp) $(if $(filter $(CC_TYPE),clang++),-include-pch $<) -o $@ $(@:.o=.cpp)
+
+# No stan/math/mix/core.hpp exists
+test/unit/math/mix/core/%.o : test/unit/math/mix/core/%.cpp
+	$(COMPILE.cpp) -o $@ $(@:.o=.cpp)
+
+
 ############################################################
 ##
 # Test generator for distribution tests
diff --git a/makefile b/makefile
index 1e88f7b5ee9..1592289b682 100644
--- a/makefile
+++ b/makefile
@@ -1,12 +1,11 @@
 # Makefile for Stan.
 ##
 
+.SUFFIXES: 
+
 # The default target of this Makefile is...
 help:
 
-## Disable implicit rules.
-SUFIXES:
-
 include make/default_compiler_options
 
 ##
@@ -46,6 +45,7 @@ include make/cpplint  # cpplint
 ##
 ifneq (,$(filter-out test-headers generate-tests clean% %-test %.d,$(MAKECMDGOALS)))
   -include $(addsuffix .d,$(subst $(EXE),,$(MAKECMDGOALS)))
+  -include $(shell find stan -name *.d)
 endif
 
 
@@ -121,11 +121,11 @@ doxygen:
 clean:
 	@echo '  removing test executables'
 	$(shell find test -type f -name "*_test$(EXE)" -exec rm {} +)
-	$(shell find test -type f -name "*_test.d" -exec rm {} +)
 	$(shell find test -type f -name "*_test.d.*" -exec rm {} +)
 	$(shell find test -type f -name "*_test.xml" -exec rm {} +)
 	$(shell find test -type f -name "*.o" -exec rm {} +)
 	$(shell find test -type f -name "lib*.so" -exec rm {} +)
+	$(shell find test stan -type f -name "*.d" -or -name "*.hpp.gch" -exec rm {} +)
 
 clean-doxygen:
 	$(RM) -r doc/api
diff --git a/runTests.py b/runTests.py
index 368ea8849ce..b72da3cf653 100755
--- a/runTests.py
+++ b/runTests.py
@@ -17,7 +17,7 @@
 
 winsfx = ".exe"
 testsfx = "_test.cpp"
-batchSize = 25
+batchSize = 32
 
 
 def processCLIArgs():