diff --git a/Makefile b/Makefile
index 59c4ef76..5c73a08b 100644
--- a/Makefile
+++ b/Makefile
@@ -190,6 +190,8 @@ $(ER7_UTILS_DIRS): icg_sim_serv
 # 1.1.1.4 Generate interface code (using ICG) for the specified sim_services
 # header files.
 .PHONY: icg_sim_serv
+# Replace -isystem with -I so ICG doesn't skip Trick headers
+icg_sim_serv: TRICK_SYSTEM_CXXFLAGS := $(subst -isystem,-I,$(TRICK_SYSTEM_CXXFLAGS))
 icg_sim_serv: $(ICG_EXE)
 	${ICG_EXE} -sim_services -m ${TRICK_CXXFLAGS} ${TRICK_SYSTEM_CXXFLAGS} ${TRICK_HOME}/include/trick/files_to_ICG.hh
 
@@ -469,6 +471,8 @@ uninstall:
 ################################################################################
 # ICG all sim_services files (for testing and debugging ICG).
 # The -f flag forces io_src files to be regenerated whether or not they need to be.
+# Replace -isystem with -I so ICG doesn't skip Trick headers
+ICG: TRICK_SYSTEM_CXXFLAGS := $(subst -isystem,-I,$(TRICK_SYSTEM_CXXFLAGS))
 ICG: $(ICG_EXE)
 	$(ICG_EXE) -f -s -m -n ${TRICK_CXXFLAGS} ${TRICK_SYSTEM_CXXFLAGS} ${TRICK_HOME}/include/trick/files_to_ICG.hh
 
diff --git a/autoconf/configure.ac b/autoconf/configure.ac
index 667f1887..1a22a090 100644
--- a/autoconf/configure.ac
+++ b/autoconf/configure.ac
@@ -410,7 +410,7 @@ AX_COMPARE_VERSION(
   [PYTHON_LIBS_COMMAND="${PYTHON_LIBS_COMMAND} --embed"]
 )
 
-PYTHON_CPPFLAGS=`${PYTHON_CONFIG} --includes`
+PYTHON_CPPFLAGS=`${PYTHON_CONFIG} --includes | sed 's/-I/-isystem/g'`
 PYTHON_LIBS=`${PYTHON_LIBS_COMMAND}`
 
 AC_SUBST([PYTHON_CPPFLAGS])
diff --git a/configure b/configure
index 6775975c..171d4e3f 100755
--- a/configure
+++ b/configure
@@ -5599,7 +5599,7 @@ x$ax_compare_version_B" | sed 's/^ *//' | sort -r | sed "s/x${ax_compare_version
       fi
 
 
-PYTHON_CPPFLAGS=`${PYTHON_CONFIG} --includes`
+PYTHON_CPPFLAGS=`${PYTHON_CONFIG} --includes | sed 's/-I/-isystem/g'`
 PYTHON_LIBS=`${PYTHON_LIBS_COMMAND}`
 
 
diff --git a/libexec/trick/pm/parse_s_define.pm b/libexec/trick/pm/parse_s_define.pm
index 4c609891..c0313c50 100644
--- a/libexec/trick/pm/parse_s_define.pm
+++ b/libexec/trick/pm/parse_s_define.pm
@@ -176,7 +176,7 @@ sub parse_s_define ($) {
 
     my @preprocess_output;
 
-    @{$$sim_ref{inc_paths}} = (get_include_paths(), $ENV{TRICK_SYSTEM_CFLAGS} =~ /-I(\S+)/g, "$ENV{TRICK_HOME}/trick_source" , "../include") ;
+    @{$$sim_ref{inc_paths}} = (get_include_paths(), $ENV{TRICK_SYSTEM_CFLAGS} =~ /-(?:I|isystem)(\S+)/g, "$ENV{TRICK_HOME}/trick_source" , "../include") ;
 
     my @valid_inc_paths ;
     foreach (@{$$sim_ref{inc_paths}}) {
diff --git a/share/trick/makefiles/Makefile.common b/share/trick/makefiles/Makefile.common
index ccc2ebb1..8a84fa6b 100644
--- a/share/trick/makefiles/Makefile.common
+++ b/share/trick/makefiles/Makefile.common
@@ -90,7 +90,7 @@ else
     LIBEXEC = lib
 endif
 
-TRICK_INCLUDES := -I${TRICK_HOME}/trick_source -I${TRICK_HOME}/include -I${TRICK_HOME}/include/trick/compat
+TRICK_INCLUDES := -isystem${TRICK_HOME}/trick_source -isystem${TRICK_HOME}/include -isystem${TRICK_HOME}/include/trick/compat
 TRICK_VERSIONS := -DTRICK_VER=$(TRICK_MAJOR) -DTRICK_MINOR=$(TRICK_MINOR)
 
 export TRICK_SYSTEM_CXXFLAGS := $(TRICK_INCLUDES) $(TRICK_VERSIONS) -fpic $(UDUNITS_INCLUDES)
@@ -190,8 +190,8 @@ export TRICK_SYSTEM_CFLAGS := $(TRICK_SYSTEM_CXXFLAGS) -fexceptions
 TRICK_SYSTEM_CFLAGS   += $(TRICK_ADDITIONAL_CFLAGS)
 TRICK_SYSTEM_CXXFLAGS += $(TRICK_ADDITIONAL_CXXFLAGS)
 
-TRICK_INCLUDE  = $(shell $(PERL) -e '@inc_paths = "${TRICK_CFLAGS}" =~ /-I\s*(\S+)/g ; foreach $$i (@inc_paths) { print "-I$$i " if (-e $$i and $$i ne "/usr/include")}') \
-                 $(shell $(PERL) -e '@inc_paths = "${TRICK_SYSTEM_CFLAGS}" =~ /-I\s*(\S+)/g ; foreach $$i (@inc_paths) { print "-I$$i " if (-e $$i)}')
+TRICK_INCLUDE  = $(shell $(PERL) -e '@inc_paths = "${TRICK_CFLAGS}" =~ /-(?:I|isystem)\s*(\S+)/g ; foreach $$i (@inc_paths) { print "-I$$i " if (-e $$i and $$i ne "/usr/include")}') \
+                 $(shell $(PERL) -e '@inc_paths = "${TRICK_SYSTEM_CFLAGS}" =~ /-(?:I|isystem)\s*(\S+)/g ; foreach $$i (@inc_paths) { print "-I$$i " if (-e $$i)}')
 
 TRICK_DEFINES  = $(shell $(PERL) -e '@defines = "${TRICK_CFLAGS}" =~ /-D\s*(\S+)/g ; foreach $$i (@defines) { print "-D$$i "}') \
                  $(shell $(PERL) -e '@defines = "${TRICK_SYSTEM_CFLAGS}" =~ /-D\s*(\S+)/g ; foreach $$i (@defines) { print "-D$$i "}')
diff --git a/share/trick/makefiles/config_user_cmake.mk.in b/share/trick/makefiles/config_user_cmake.mk.in
index 44f7bd76..b745a321 100644
--- a/share/trick/makefiles/config_user_cmake.mk.in
+++ b/share/trick/makefiles/config_user_cmake.mk.in
@@ -31,7 +31,7 @@ ICG_CLANGLIBS = \
     -lclangLex \
     -lclangBasic \
 
-PYTHON_INCLUDES = -I@PYTHON_INCLUDE_DIRS@
+PYTHON_INCLUDES = -isystem@PYTHON_INCLUDE_DIRS@
 PYTHON_LIB = @PYTHON_LIBRARIES@
 
 # Only add udunits include if it is not in /usr/include.
diff --git a/trick_source/sim_services/MemoryManager/test/Makefile b/trick_source/sim_services/MemoryManager/test/Makefile
index f55b6ae4..6ffd6553 100644
--- a/trick_source/sim_services/MemoryManager/test/Makefile
+++ b/trick_source/sim_services/MemoryManager/test/Makefile
@@ -7,6 +7,9 @@
 
 include $(dir $(lastword $(MAKEFILE_LIST)))../../../../share/trick/makefiles/Makefile.common
 
+# Replace -isystem with -I so ICG doesn't skip Trick headers
+TRICK_SYSTEM_CXXFLAGS := $(subst -isystem,-I,$(TRICK_SYSTEM_CXXFLAGS))
+
 #COVERAGE_FLAGS += -fprofile-arcs -ftest-coverage -O0
 #TRICK_SYSTEM_LDFLAGS  += ${COVERAGE_FLAGS}