diff --git a/configure.ac b/configure.ac
index d8e14bb..1b3fb93 100644
--- a/configure.ac
+++ b/configure.ac
@@ -333,7 +333,7 @@ if test -z "$HDF5ROOT"; then
 	exit 1
 fi
 
-INCLUDES="$INCLUDES -I$HDF5ROOT/include"
+AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5ROOT/include"
 LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
 LIBS="$LIBS -lhdf5"
 
@@ -370,7 +370,7 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        INCLUDES="$INCLUDES -I$LUSTREROOT/usr/include"
+        AM_CPPFLAGS=="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
         LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
@@ -401,7 +401,7 @@ AC_SUBST(HDF5ROOT)
 AC_SUBST(LUSTREROOT)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(INCLUDES)
+AC_SUBST(AM_CPPFLAGS)
 AC_SUBST(LDFLAGS)
 AC_SUBST(LIBS)
 AC_SUBST(UNDERSCORE_H)
diff --git a/src/C++/Makefile.am b/src/C++/Makefile.am
index 3f24f4b..66b1bb3 100644
--- a/src/C++/Makefile.am
+++ b/src/C++/Makefile.am
@@ -3,7 +3,7 @@ CC = @CC@
 CXX = @CXX@
 
 LIBS = @LIBS@
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 OBJEXT = o
 
diff --git a/src/C/Makefile.am b/src/C/Makefile.am
index 2effd7c..fbffbb1 100644
--- a/src/C/Makefile.am
+++ b/src/C/Makefile.am
@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 # What to build... Will be determined by configure script.
 lib_LTLIBRARIES = @LIB_C@
diff --git a/src/Fortran/Makefile.am b/src/Fortran/Makefile.am
index b20fcc4..0fbb6c2 100644
--- a/src/Fortran/Makefile.am
+++ b/src/Fortran/Makefile.am
@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 F90_FILES =     	H5.f90 \
 			H5_attribs.f90 \
diff --git a/src/h5core/Makefile.am b/src/h5core/Makefile.am
index f25ce42..5c040aa 100644
--- a/src/h5core/Makefile.am
+++ b/src/h5core/Makefile.am
@@ -2,7 +2,7 @@
 
 OBJEXT=o
 
-INCLUDES = -I../include @INCLUDES@
+AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
 
 EXTRA_HEADERS =					\
 	../include/h5core/h5_attach.h		\
diff --git a/test/H5Fed/Makefile.am b/test/H5Fed/Makefile.am
index 814c839..71cb56c 100644
--- a/test/H5Fed/Makefile.am
+++ b/test/H5Fed/Makefile.am
@@ -4,7 +4,7 @@ OBJEXT = o
 
 AM_LDFLAGS = -L../../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
-INCLUDES = -I../../src/include @INCLUDES@
+AM_CPPFLAGS = -I../../src/include @AM_CPPFLAGS@
 
 noinst_PROGRAMS =				\
 		tetmesh_write			\
diff --git a/test/Makefile.am b/test/Makefile.am
index 55a325b..6b72a73 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -5,7 +5,7 @@ SUBDIRS = H5Fed
 
 OBJEXT=o
 
-INCLUDES = -I../src/include @INCLUDES@
+AM_LDFLAGS = -I../src/include @AM_CPPFLAGS@
 
 noinst_PROGRAMS = @BUILD_TESTS@
 
diff --git a/tools/Makefile.am b/tools/Makefile.am
index 09f5dec..362cea0 100644
--- a/tools/Makefile.am
+++ b/tools/Makefile.am
@@ -9,7 +9,7 @@ endif
 AM_LDFLAGS = -L../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
-INCLUDES = -I../src/include @INCLUDES@
+AM_CPPFLAGS = -I../src/include @AM_CPPFLAGS@
 
 # What to build... make install will place these files in the $(prefix)/bin directory.
 bin_PROGRAMS = @BUILD_TOOLS@