Index: glibc/files/eblits/src_install.eblit
===================================================================
--- glibc.orig/files/eblits/src_install.eblit
+++ glibc/files/eblits/src_install.eblit
@@ -10,7 +10,7 @@ toolchain-glibc_src_install() {
 		GBUILDDIR=${WORKDIR}/build-${ABI}-${CTARGET}-nptl
 	fi
 
-	local install_root="${D}$(alt_prefix)"
+	local install_root="${D}${EPREFIX%${TPREFIX}}/$(alt_prefix)"
 	if want_linuxthreads ; then
 		cd "${WORKDIR}"/build-${ABI}-${CTARGET}-linuxthreads
 		einfo "Installing GLIBC ${ABI} with linuxthreads ..."
@@ -190,7 +190,7 @@ toolchain-glibc_src_install() {
 toolchain-glibc_headers_install() {
 	local GBUILDDIR=${WORKDIR}/build-${ABI}-${CTARGET}-headers
 	cd "${GBUILDDIR}"
-	emake install_root="${D}$(alt_prefix)" install-headers || die
+	emake install_root="${D}${EPREFIX%${TPREFIX}}/$(alt_prefix)" install-headers || die
 	if ! version_is_at_least 2.16 ; then
 		insinto $(alt_headers)/bits
 		doins bits/stdio_lim.h || die
Index: glibc/files/eblits/src_compile.eblit
===================================================================
--- glibc.orig/files/eblits/src_compile.eblit
+++ glibc/files/eblits/src_compile.eblit
@@ -74,12 +74,14 @@ glibc_do_configure() {
 		--host=${CTARGET_OPT:-${CTARGET}}
 		$(use_enable profile)
 		$(use_with gd)
-		--with-headers=$(alt_build_headers)
-		--prefix=/usr
-		--libdir=/usr/$(get_libdir)
-		--mandir=/usr/share/man
-		--infodir=/usr/share/info
-		--libexecdir=/usr/$(get_libdir)/misc/glibc
+		--with-headers="${EPREFIX}$(alt_build_headers)"
+		--prefix="${TPREFIX}/usr"
+		--libdir="${TPREFIX}/usr/$(get_libdir)"
+		--mandir="${TPREFIX}/usr/share/man"
+		--infodir="${TPREFIX}/usr/share/info"
+		--libexecdir="${TPREFIX}/usr/$(get_libdir)/misc/glibc"
+		--sysconfdir="${TPREFIX}/etc"
+		--localstatedir="${TPREFIX}/var"
 		--with-bugurl=http://bugs.gentoo.org/
 		--with-pkgversion="$(glibc_banner)"
 		$(use_multiarch || echo --disable-multi-arch)
@@ -91,7 +93,7 @@ glibc_do_configure() {
 
 	# There is no configure option for this and we need to export it
 	# since the glibc build will re-run configure on itself
-	export libc_cv_slibdir=/$(get_libdir)
+	export libc_cv_slibdir="${TPREFIX}/$(get_libdir)"
 
 	# We take care of patching our binutils to use both hash styles,
 	# and many people like to force gnu hash style only, so disable
@@ -199,8 +201,8 @@ toolchain-glibc_headers_compile() {
 		--enable-bind-now
 		--build=${CBUILD_OPT:-${CBUILD}}
 		--host=${CTARGET_OPT:-${CTARGET}}
-		--with-headers=$(alt_build_headers)
-		--prefix=/usr
+		--with-headers="${EPREFIX}$(alt_build_headers)"
+		--prefix="${TPREFIX}/usr"
 		${EXTRA_ECONF}
 	)
 
Index: glibc/files/eblits/common.eblit
===================================================================
--- glibc.orig/files/eblits/common.eblit
+++ glibc/files/eblits/common.eblit
@@ -2,10 +2,28 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sys-libs/glibc/files/eblits/common.eblit,v 1.29 2012/12/28 19:00:51 vapier Exp $
 
+# There are many directory offsets here that can lead to confusion. We summarize the senarios in this table
+# P:=Prefix X:=Cross-Triplet
+# example of configure host: --with-headers
+# example of configure target: --libdir
+#
+# variation   phase               PX                      X               P         solution
+# -----------+-------------------+-----------------------+---------------+---------+----------------------------------------
+# host        configure           EPREFIX/usr/CTARGET     /usr/CTARGET    EPREFIX   $EPREFIX/$(alt_prefix)
+# target      configure           NULL                    NULL            EPREFIX   $TPREFIX
+# -----------+-------------------+-----------------------+---------------+---------+----------------------------------------
+# host        install_root        D/EPREFIX/usr/CTARGET   D/usr/CTARGET   D         ${D}/${EPREFIX%$TPREFIX}/$(alt_prefix)
+# -----------+-------------------+-----------------------+---------------+---------+----------------------------------------
+# host        ebuild helper ED/   /usr/CTARGET            /usr/CTARGET    NULL      $(alt_prefix)
+#
+# alt_prefix and TPREFIX in the table are defined as followed
+
 alt_prefix() {
 	is_crosscompile && echo /usr/${CTARGET}
 }
 
+TPREFIX=$(is_crosscompile || echo "${EPREFIX}")
+
 : ${ED:=${D}}
 : ${EROOT:=${ROOT}}
 
@@ -22,7 +40,7 @@ alt_build_headers() {
 		ALT_BUILD_HEADERS=$(alt_headers)
 		if tc-is-cross-compiler ; then
 			ALT_BUILD_HEADERS=${ROOT}$(alt_headers)
-			if [[ ! -e ${ALT_BUILD_HEADERS}/linux/version.h ]] ; then
+			if [[ ! -e ${EPREFIX}/${ALT_BUILD_HEADERS}/linux/version.h ]] ; then
 				local header_path=$(echo '#include <linux/version.h>' | $(tc-getCPP ${CTARGET}) ${CFLAGS} 2>&1 | grep -o '[^"]*linux/version.h')
 				ALT_BUILD_HEADERS=${header_path%/linux/version.h}
 			fi