diff --git a/Makefile.am b/Makefile.am
index bce84b91..82101c57 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -12,49 +12,49 @@ dist-hook:
 	grep "^#enable_debug=" configure
 
 # Preprocessor flags.
-CPPFLAGS += @XOPEN_DEFINES@ -DTMUX_CONF="\"$(sysconfdir)/tmux.conf\""
+AM_CPPFLAGS += @XOPEN_DEFINES@ -DTMUX_CONF="\"$(sysconfdir)/tmux.conf\""
 
 # glibc as usual does things ass-backwards and hides useful things by default,
 # so everyone has to add this.
 if IS_GLIBC
-CFLAGS += -D_GNU_SOURCE
+AM_CFLAGS += -D_GNU_SOURCE
 endif
 
 # Set flags for gcc.
 if IS_GCC
-CFLAGS += -std=gnu99 -O2
+AM_CFLAGS += -std=gnu99 -O2
 if IS_DEBUG
-CFLAGS += -g
-CFLAGS += -Wno-long-long -Wall -W -Wformat=2
-CFLAGS += -Wmissing-prototypes -Wstrict-prototypes -Wmissing-declarations
-CFLAGS += -Wwrite-strings -Wshadow -Wpointer-arith -Wsign-compare
-CFLAGS += -Wundef -Wbad-function-cast -Winline -Wcast-align
-CFLAGS += -Wdeclaration-after-statement -Wno-pointer-sign -Wno-attributes
-CPPFLAGS += -DDEBUG
+AM_CFLAGS += -g
+AM_CFLAGS += -Wno-long-long -Wall -W -Wformat=2
+AM_CFLAGS += -Wmissing-prototypes -Wstrict-prototypes -Wmissing-declarations
+AM_CFLAGS += -Wwrite-strings -Wshadow -Wpointer-arith -Wsign-compare
+AM_CFLAGS += -Wundef -Wbad-function-cast -Winline -Wcast-align
+AM_CFLAGS += -Wdeclaration-after-statement -Wno-pointer-sign -Wno-attributes
+AM_CPPFLAGS += -DDEBUG
 endif
 if IS_COVERAGE
-CFLAGS += -g -O0 --coverage
-LDFLAGS += --coverage
+AM_CFLAGS += -g -O0 --coverage
+AM_LDFLAGS += --coverage
 endif
 if IS_PROFILE
-CFLAGS += -g -O0 -pg
-LDFLAGS += -pg
+AM_CFLAGS += -g -O0 -pg
+AM_LDFLAGS += -pg
 endif
-CPPFLAGS += -iquote.
+AM_CPPFLAGS += -iquote.
 endif
 
 # Set flags for Solaris.
 if IS_SUNOS
 if IS_GCC
-CPPFLAGS += -D_XPG6 -D__EXTENSIONS__ -D_POSIX_PTHREAD_SEMANTICS
+AM_CPPFLAGS += -D_XPG6 -D__EXTENSIONS__ -D_POSIX_PTHREAD_SEMANTICS
 else
-CPPFLAGS += -D_XPG4_2 -D__EXTENSIONS__ -D_POSIX_PTHREAD_SEMANTICS
+AM_CPPFLAGS += -D_XPG4_2 -D__EXTENSIONS__ -D_POSIX_PTHREAD_SEMANTICS
 endif
 endif
 
 # Set flags for Sun CC.
 if IS_SUNCC
-CFLAGS += -erroff=E_EMPTY_DECLARATION
+AM_CFLAGS += -erroff=E_EMPTY_DECLARATION
 endif
 
 # Set _LINUX_SOURCE_COMPAT for AIX for malloc(0).
@@ -64,7 +64,7 @@ endif
 
 # Set flags for NetBSD.
 if IS_NETBSD
-CPPFLAGS += -D_OPENBSD_SOURCE
+AM_CPPFLAGS += -D_OPENBSD_SOURCE
 endif
 
 # List of sources.
diff --git a/configure.ac b/configure.ac
index c172d6b2..c43a87e1 100644
--- a/configure.ac
+++ b/configure.ac
@@ -12,6 +12,13 @@ AC_CANONICAL_HOST
 # empty default.
 : ${CFLAGS=""}
 
+# Save user CPPFLAGS, CFLAGS and LDFLAGS. We need to change them because
+# AC_CHECK_HEADER doesn't give us any other way to update the include
+# paths. But for Makefile.am we want to use AM_CPPFLAGS and friends.
+SAVED_CFLAGS="$CFLAGS"
+SAVED_CPPFLAGS="$CPPFLAGS"
+SAVED_LDFLAGS="$LDFLAGS"
+
 # Set up the compiler in two different ways and say yes we may want to install.
 AC_PROG_CC
 AM_PROG_CC_C_O
@@ -51,8 +58,9 @@ AC_ARG_ENABLE(
 	AC_HELP_STRING(--enable-static, create a static build)
 )
 if test "x$enable_static" = xyes; then
-	LDFLAGS="$LDFLAGS -static"
 	test "x$PKG_CONFIG" != x && PKG_CONFIG="$PKG_CONFIG --static"
+	AM_LDFLAGS="-static $AM_LDFLAGS"
+	LDFLAGS="$AM_LDFLAGS $SAVED_LDFLAGS"
 fi
 
 # Is this gcc?
@@ -129,7 +137,8 @@ PKG_CHECK_MODULES(
 	LIBEVENT,
 	libevent,
 	[
-		CPPFLAGS="$LIBEVENT_CFLAGS $CPPFLAGS"
+		AM_CFLAGS="$LIBEVENT_CFLAGS $AM_CFLAGS"
+		CFLAGS="$AM_CFLAGS $SAVED_CFLAGS"
 		LIBS="$LIBEVENT_LIBS $LIBS"
 		found_libevent=yes
 	],
@@ -156,7 +165,8 @@ PKG_CHECK_MODULES(
 	LIBNCURSES,
 	ncurses,
 	[
-		CPPFLAGS="$LIBNCURSES_CFLAGS $CPPFLAGS"
+		AM_CFLAGS="$LIBNCURSES_CFLAGS $AM_CFLAGS"
+		CFLAGS="$AM_CFLAGS $SAVED_CFLAGS"
 		LIBS="$LIBNCURSES_LIBS $LIBS"
 		found_ncurses=yes
 	],
@@ -645,5 +655,14 @@ AM_CONDITIONAL(IS_SUNOS, test "x$PLATFORM" = xsunos)
 AM_CONDITIONAL(IS_HPUX, test "x$PLATFORM" = xhpux)
 AM_CONDITIONAL(IS_UNKNOWN, test "x$PLATFORM" = xunknown)
 
+# Save our CFLAGS/CPPFLAGS/LDFLAGS for the Makefile and restore the old user
+# variables.
+AC_SUBST(AM_CPPFLAGS)
+CPPFLAGS="$SAVED_CPPFLAGS"
+AC_SUBST(AM_CFLAGS)
+CFLAGS="$SAVED_CFLAGS"
+AC_SUBST(AM_LDFLAGS)
+LDFLAGS="$SAVED_LDFLAGS"
+
 # autoconf should create a Makefile.
 AC_OUTPUT(Makefile)