diff --git a/acinclude.m4 b/acinclude.m4
index cdc6fdeb5..c9213e48d 100644
--- a/acinclude.m4
+++ b/acinclude.m4
@@ -1,15 +1,15 @@
 dnl
 dnl Contains the following macros
-dnl   SANE_SET_CFLAGS(is_release)
+dnl   SANE_SET_AM_CFLAGS(is_release)
 dnl   SANE_CHECK_MISSING_HEADERS
-dnl   SANE_SET_LDFLAGS
+dnl   SANE_SET_AM_LDFLAGS
 dnl   SANE_CHECK_DLL_LIB
 dnl   SANE_EXTRACT_LDFLAGS(LIBS, LDFLAGS)
 dnl   SANE_CHECK_JPEG
 dnl   SANE_CHECK_IEEE1284
 dnl   SANE_CHECK_PTHREAD
 dnl   SANE_CHECK_LOCKING
-dnl   JAPHAR_GREP_CFLAGS(flag, cmd_if_missing, cmd_if_present)
+dnl   JAPHAR_GREP_AM_CFLAGS(flag, cmd_if_missing, cmd_if_present)
 dnl   SANE_LINKER_RPATH
 dnl   SANE_CHECK_U_TYPES
 dnl   SANE_CHECK_GPHOTO2
@@ -19,12 +19,12 @@ dnl   SANE_PROTOTYPES
 dnl   AC_PROG_LIBTOOL
 dnl
 
-# SANE_SET_CFLAGS(is_release)
-# Set default CFLAGS if gcc is used.  Enable or disable additional
+# SANE_SET_AM_CFLAGS(is_release)
+# Set default AM_CFLAGS if gcc is used.  Enable/disable additional
 # compilation warnings.  The extra warnings are enabled by default
 # during the development cycle but disabled for official releases.
 # The argument is_release is either yes or no.
-AC_DEFUN([SANE_SET_CFLAGS],
+AC_DEFUN([SANE_SET_AM_CFLAGS],
 [
 if test "${ac_cv_c_compiler_gnu}" = "yes"; then
   DEFAULT_CFLAGS="\
@@ -35,7 +35,7 @@ if test "${ac_cv_c_compiler_gnu}" = "yes"; then
       -pedantic"
 
   for flag in $DEFAULT_CFLAGS; do
-    JAPHAR_GREP_CFLAGS($flag, [ CFLAGS="$CFLAGS $flag" ])
+    JAPHAR_GREP_AM_CFLAGS($flag, [ AM_CFLAGS="$AM_CFLAGS $flag" ])
   done
 
   AC_ARG_ENABLE(warnings,
@@ -44,14 +44,14 @@ if test "${ac_cv_c_compiler_gnu}" = "yes"; then
     [
       if eval "test x$enable_warnings = xyes"; then 
         for flag in $EXTRA_WARNINGS; do
-          JAPHAR_GREP_CFLAGS($flag, [ CFLAGS="$CFLAGS $flag" ])
+          JAPHAR_GREP_AM_CFLAGS($flag, [ AM_CFLAGS="$AM_CFLAGS $flag" ])
         done
       fi
     ],
     [if test x$1 = xno; then
        # Warnings enabled by default (development)
        for flag in $EXTRA_WARNINGS; do
-         JAPHAR_GREP_CFLAGS($flag, [ CFLAGS="$CFLAGS $flag" ])
+         JAPHAR_GREP_AM_CFLAGS($flag, [ AM_CFLAGS="$AM_CFLAGS $flag" ])
        done
     fi])
 fi # ac_cv_c_compiler_gnu
@@ -84,9 +84,9 @@ AC_DEFUN([SANE_CHECK_MISSING_HEADERS],
   fi
 ])
 
-# SANE_SET_LDFLAGS
-# Add special LDFLAGS
-AC_DEFUN([SANE_SET_LDFLAGS],
+# SANE_SET_AM_LDFLAGS
+# Add special AM_LDFLAGS
+AC_DEFUN([SANE_SET_AM_LDFLAGS],
 [
   # Define stricter linking policy on GNU systems.  This is not
   # added to global LDFLAGS because we may want to create convenience
@@ -101,7 +101,7 @@ AC_DEFUN([SANE_SET_LDFLAGS],
   AC_SUBST(STRICT_LDFLAGS)
   case "${host_os}" in  
     aix*) #enable .so libraries, disable archives
-      LDFLAGS="$LDFLAGS -Wl,-brtl"
+      AM_LDFLAGS="$AM_LDFLAGS -Wl,-brtl"
       ;;
     darwin*) #include frameworks
       LIBS="$LIBS -framework CoreFoundation -framework IOKit"
@@ -245,7 +245,7 @@ AC_DEFUN([SANE_CHECK_PTHREAD],
     PTHREAD_LIBS=""
   fi
   if test "$have_pthread" = "yes" ; then
-    CPPFLAGS="${CPPFLAGS} -D_REENTRANT"
+    AM_CPPFLAGS="${AM_CPPFLAGS} -D_REENTRANT"
   fi
   AC_SUBST(PTHREAD_LIBS)
   AC_MSG_CHECKING([whether to enable pthread support])
@@ -362,12 +362,12 @@ AC_DEFUN([SANE_CHECK_LOCKING],
 ])
 
 dnl
-dnl JAPHAR_GREP_CFLAGS(flag, cmd_if_missing, cmd_if_present)
+dnl JAPHAR_GREP_AM_CFLAGS(flag, cmd_if_missing, cmd_if_present)
 dnl
 dnl From Japhar.  Report changes to japhar@hungry.com
 dnl
-AC_DEFUN([JAPHAR_GREP_CFLAGS],
-[case "$CFLAGS" in
+AC_DEFUN([JAPHAR_GREP_AM_CFLAGS],
+[case "$AM_CFLAGS" in
 "$1" | "$1 "* | *" $1" | *" $1 "* )
   ifelse($#, 3, [$3], [:])
   ;;
diff --git a/backend/Makefile.am b/backend/Makefile.am
index 82f147952..3abba6f05 100644
--- a/backend/Makefile.am
+++ b/backend/Makefile.am
@@ -4,9 +4,9 @@
 ##  This file is part of the "Sane" build infra-structure.  See
 ##  included LICENSE file for license information.
 
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include -DLIBDIR="\"$(libdir)/sane\""
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include -DLIBDIR="\"$(libdir)/sane\""
 
-AM_LDFLAGS = $(STRICT_LDFLAGS)
+AM_LDFLAGS += $(STRICT_LDFLAGS)
 # The -rpath option is added because we are creating _LTLIBRARIES based
 # on configure substitution.  This causes automake to not know the
 # correct $libdir and must be added here.
diff --git a/configure.ac b/configure.ac
index 07ccae636..b49e00551 100644
--- a/configure.ac
+++ b/configure.ac
@@ -82,8 +82,8 @@ AM_CONDITIONAL(CROSS_COMPILING, test x$cross_compiling = xyes)
 dnl ***********************************************************************
 dnl set compiler/linker flags
 dnl ***********************************************************************
-SANE_SET_CFLAGS([$is_release])
-SANE_SET_LDFLAGS
+SANE_SET_AM_CFLAGS([$is_release])
+SANE_SET_AM_LDFLAGS
 SANE_LINKER_RPATH
 
 dnl ***********************************************************************
@@ -414,7 +414,7 @@ if test "$enable_libusb" != "no"; then
   if test "$enable_libusb_1_0" = "yes"; then
     PKG_CHECK_MODULES(LIBUSB_1_0, [ libusb-1.0 >= 1.0.0 ], have_libusb_1_0=yes, have_libusb_1_0=no)
     if test "$have_libusb_1_0" = "yes"; then
-      CFLAGS="$CFLAGS $LIBUSB_1_0_CFLAGS"
+      AM_CFLAGS="$AM_CFLAGS $LIBUSB_1_0_CFLAGS"
       USB_LIBS="$USB_LIBS $LIBUSB_1_0_LIBS"
       HAVE_USB=yes
     fi
@@ -561,7 +561,7 @@ AC_ARG_ENABLE(scsi-directio,
                   README.linux)]),
   [
     if eval "test x$enable_scsi_directio = xyes"; then
-      CFLAGS="$CFLAGS -DENABLE_SCSI_DIRECTIO"
+      AM_CFLAGS="$AM_CFLAGS -DENABLE_SCSI_DIRECTIO"
     fi
   ])
 
@@ -592,7 +592,7 @@ AC_PROG_LIBTOOL
 dnl Windows (cygwin/mingw), BeOS, and OS/2 need this.
 case $host_os in
   cygwin* | mingw* | beos* | os2*)
-  LDFLAGS="$LDFLAGS -no-undefined"
+  AM_LDFLAGS="$AM_LDFLAGS -no-undefined"
 esac
 
 dnl Check for lock dir
@@ -610,7 +610,7 @@ dnl enable/disable backends and features based on previous tests and user's
 dnl choice
 dnl ***********************************************************************
 
-CPPFLAGS="${CPPFLAGS} -DPATH_SANE_CONFIG_DIR=\$(configdir) \
+AM_CPPFLAGS="${AM_CPPFLAGS} -DPATH_SANE_CONFIG_DIR=\$(configdir) \
 	  -DPATH_SANE_DATA_DIR=\$(datadir) \
 	  -DPATH_SANE_LOCK_DIR=\$(locksanedir) \
 	  -DV_MAJOR=${V_MAJOR} -DV_MINOR=${V_MINOR}"
@@ -762,7 +762,7 @@ AC_ARG_ENABLE(parport-directio,
                   frontends will require special permission level]),
   [
     if eval "test x$enable_parport_directio = xyes"; then
-      CFLAGS="$CFLAGS -DENABLE_PARPORT_DIRECTIO"
+      AM_CFLAGS="$AM_CFLAGS -DENABLE_PARPORT_DIRECTIO"
     fi
   ])
 
@@ -802,6 +802,10 @@ dnl ***********************************************************************
 dnl Write output files
 dnl ***********************************************************************
 
+AC_SUBST(AM_CPPFLAGS)
+AC_SUBST(AM_CFLAGS)
+AC_SUBST(AM_LDFLAGS)
+
 DISTCLEAN_FILES="*~ .*~ *.log *.bak *.old *.orig *.out *.rej \"\#\"* \".\\#\"*"
 AC_SUBST(DISTCLEAN_FILES)
 
@@ -818,9 +822,9 @@ dnl print configuration information
 dnl ***********************************************************************
 
 echo "-> Variables used for compilation/linking:"
-echo CPPFLAGS=\"${CPPFLAGS}\"
-echo CFLAGS=\"${CFLAGS}\"
-echo LDFLAGS=\"${LDFLAGS}\"
+echo AM_CPPFLAGS=\"${AM_CPPFLAGS}\"
+echo AM_CFLAGS=\"${AM_CFLAGS}\"
+echo AM_LDFLAGS=\"${AM_LDFLAGS}\"
 echo LIBS=\"${LIBS}\"
 echo "-> Installation directories:"
 echo "Configuration: `eval eval echo ${sysconfdir}`"
diff --git a/frontend/Makefile.am b/frontend/Makefile.am
index 22448b691..adb1dd47f 100644
--- a/frontend/Makefile.am
+++ b/frontend/Makefile.am
@@ -14,7 +14,7 @@ else
 EXTRA_PROGRAMS += saned
 endif
 
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include
 
 scanimage_SOURCES = scanimage.c stiff.c stiff.h
 scanimage_LDADD = ../backend/libsane.la ../sanei/libsanei.la ../lib/liblib.la \
diff --git a/japi/Makefile.am b/japi/Makefile.am
index 24465d6d8..8faae6c73 100644
--- a/japi/Makefile.am
+++ b/japi/Makefile.am
@@ -13,10 +13,10 @@ CLASSPATH_ENV=.
 JAVAH=javah -jni -cp $(CLASSPATH_ENV)
 
 #	We'll need something in 'configure' for the Java includes.
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include \
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include \
 	      -I$(top_srcdir)/include -I${JDK_HOME}/include \
 	      -I${JDK_HOME}/include/genunix
-AM_LDFLAGS = $(STRICT_LDFLAGS) -version-number $(V_MAJOR):$(V_MINOR):$(VREV)
+AM_LDFLAGS += $(STRICT_LDFLAGS) -version-number $(V_MAJOR):$(V_MINOR):$(VREV)
 
 JAVA_SRC = SaneDevice.java SaneOption.java SaneRange.java\
 	   Sane.java SaneParameters.java ScanIt.java \
diff --git a/lib/Makefile.am b/lib/Makefile.am
index d6e2135ae..23c883290 100644
--- a/lib/Makefile.am
+++ b/lib/Makefile.am
@@ -3,7 +3,7 @@
 ##
 ##  This file is part of the "Sane" build infra-structure.  See
 ##  included LICENSE file for license information.
-AM_CPPFLAGS = -I. -I$(top_builddir)/include -I$(top_srcdir)/include
+AM_CPPFLAGS += -I. -I$(top_builddir)/include -I$(top_srcdir)/include
 
 noinst_LTLIBRARIES = liblib.la libfelib.la
 
diff --git a/sanei/Makefile.am b/sanei/Makefile.am
index c1106ae1c..6869f5d1f 100644
--- a/sanei/Makefile.am
+++ b/sanei/Makefile.am
@@ -4,7 +4,7 @@
 ##  This file is part of the "Sane" build infra-structure.  See
 ##  included LICENSE file for license information.
 
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include \
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include \
  -I$(top_srcdir)/include
 
 noinst_LTLIBRARIES = libsanei.la
diff --git a/testsuite/sanei/Makefile.am b/testsuite/sanei/Makefile.am
index 110a7d08d..bb6d0f1b9 100644
--- a/testsuite/sanei/Makefile.am
+++ b/testsuite/sanei/Makefile.am
@@ -15,7 +15,7 @@ TEST_LDADD = ../../sanei/libsanei.la ../../lib/liblib.la ../../lib/libfelib.la $
 check_PROGRAMS = sanei_usb_test test_wire sanei_check_test sanei_config_test sanei_constrain_test
 TESTS = $(check_PROGRAMS)
 
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include -I$(top_srcdir)/include
 
 sanei_constrain_test_SOURCES = sanei_constrain_test.c
 sanei_constrain_test_LDADD = $(TEST_LDADD)
diff --git a/tools/Makefile.am b/tools/Makefile.am
index b24d85af3..2593505ad 100644
--- a/tools/Makefile.am
+++ b/tools/Makefile.am
@@ -4,7 +4,7 @@
 ##  This file is part of the "Sane" build infra-structure.  See
 ##  included LICENSE file for license information.
 
-AM_CPPFLAGS = -I. -I$(srcdir) -I$(top_builddir)/include \
+AM_CPPFLAGS += -I. -I$(srcdir) -I$(top_builddir)/include \
  -I$(top_srcdir)/include
 
 bin_PROGRAMS = sane-find-scanner gamma4scanimage