diff --git a/pkgs/development/tools/misc/patchelf/default.nix b/pkgs/development/tools/misc/patchelf/default.nix
index 06b5c2ef516d..5aa81e46bed1 100644
--- a/pkgs/development/tools/misc/patchelf/default.nix
+++ b/pkgs/development/tools/misc/patchelf/default.nix
@@ -8,6 +8,8 @@ stdenv.mkDerivation rec {
     sha256 = "c99f84d124347340c36707089ec8f70530abd56e7827c54d506eb4cc097a17e7";
   };
 
+  setupHook = [ ./setup-hook.sh ];
+
   meta = {
     homepage = http://nixos.org/patchelf.html;
     license = "GPL";
diff --git a/pkgs/development/tools/misc/patchelf/setup-hook.sh b/pkgs/development/tools/misc/patchelf/setup-hook.sh
new file mode 100644
index 000000000000..e27d1ed5b00c
--- /dev/null
+++ b/pkgs/development/tools/misc/patchelf/setup-hook.sh
@@ -0,0 +1,18 @@
+# This setup hook calls patchelf to automatically remove unneeded
+# directories from the RPATH of every library or executable in every
+# output.
+
+if [ -z "$dontPatchELF" ]; then
+    addHook fixupOutput 'patchELF "$prefix"'
+fi
+
+patchELF() {
+    header "patching ELF executables and libraries in $prefix"
+    if [ -e "$prefix" ]; then
+        find "$prefix" \( \
+            \( -type f -a -name "*.so*" \) -o \
+            \( -type f -a -perm +0100 \) \
+            \) -print -exec patchelf --shrink-rpath '{}' \;
+    fi
+    stopNest
+}
diff --git a/pkgs/stdenv/generic/setup.sh b/pkgs/stdenv/generic/setup.sh
index d3d2d250e500..a953176127c7 100644
--- a/pkgs/stdenv/generic/setup.sh
+++ b/pkgs/stdenv/generic/setup.sh
@@ -702,19 +702,6 @@ checkPhase() {
 }
 
 
-patchELF() {
-    # Patch all ELF executables and shared libraries.
-    header "patching ELF executables and libraries"
-    if [ -e "$prefix" ]; then
-        find "$prefix" \( \
-            \( -type f -a -name "*.so*" \) -o \
-            \( -type f -a -perm +0100 \) \
-            \) -print -exec patchelf --shrink-rpath '{}' \;
-    fi
-    stopNest
-}
-
-
 patchShebangs() {
     # Rewrite all script interpreter file names (`#! /path') under the
     # specified  directory tree to paths found in $PATH.  E.g.,
@@ -886,10 +873,6 @@ _defaultFixupOutput() {
         fi
     fi
 
-    if [ "$havePatchELF" = 1 -a -z "$dontPatchELF" ]; then
-        patchELF "$prefix"
-    fi
-
     if [ -z "$dontPatchShebangs" ]; then
         patchShebangs "$prefix"
     fi
diff --git a/pkgs/stdenv/linux/default.nix b/pkgs/stdenv/linux/default.nix
index 23cccf223f4f..7169ce9f94eb 100644
--- a/pkgs/stdenv/linux/default.nix
+++ b/pkgs/stdenv/linux/default.nix
@@ -26,7 +26,6 @@ rec {
   commonPreHook =
     ''
       export NIX_ENFORCE_PURITY=1
-      havePatchELF=1
       ${if system == "x86_64-linux" then "NIX_LIB64_IN_SELF_RPATH=1" else ""}
       ${if system == "mips64el-linux" then "NIX_LIB32_IN_SELF_RPATH=1" else ""}
     '';
@@ -46,7 +45,7 @@ rec {
     builder = bootstrapFiles.sh;
 
     args =
-      if system == "armv5tel-linux" || system == "armv6l-linux" 
+      if system == "armv5tel-linux" || system == "armv6l-linux"
         || system == "armv7l-linux"
       then [ ./scripts/unpack-bootstrap-tools-arm.sh ]
       else [ ./scripts/unpack-bootstrap-tools.sh ];
@@ -69,10 +68,10 @@ rec {
   # This function builds the various standard environments used during
   # the bootstrap.
   stdenvBootFun =
-    {gcc, extraAttrs ? {}, overrides ? (pkgs: {}), extraPath ? [], fetchurl}:
+    { gcc, extraAttrs ? {}, overrides ? (pkgs: {}), extraBuildInputs ? [], fetchurl }:
 
     import ../generic {
-      inherit system config;
+      inherit system config extraBuildInputs;
       name = "stdenv-linux-boot";
       preHook =
         ''
@@ -82,7 +81,7 @@ rec {
           ${commonPreHook}
         '';
       shell = "${bootstrapTools}/bin/sh";
-      initialPath = [bootstrapTools] ++ extraPath;
+      initialPath = [ bootstrapTools ];
       fetchurlBoot = fetchurl;
       inherit gcc;
       # Having the proper 'platform' in all the stdenvs allows getting proper
@@ -208,9 +207,9 @@ rec {
       ppl = pkgs.ppl.override { stdenv = pkgs.makeStaticLibraries pkgs.stdenv; };
     };
     extraAttrs = {
-      glibc = stdenvLinuxGlibc;   # Required by gcc47 build
+      glibc = stdenvLinuxGlibc; # Required by gcc47 build
     };
-    extraPath = [ stdenvLinuxBoot1Pkgs.paxctl ];
+    extraBuildInputs = [ stdenvLinuxBoot2Pkgs.patchelf stdenvLinuxBoot1Pkgs.paxctl ];
     inherit fetchurl;
   };
 
@@ -233,7 +232,7 @@ rec {
       gcc = stdenvLinuxBoot3Pkgs.gcc.gcc;
       name = "";
     };
-    extraPath = [ stdenvLinuxBoot3Pkgs.xz ];
+    extraBuildInputs = [ stdenvLinuxBoot2Pkgs.patchelf stdenvLinuxBoot3Pkgs.xz ];
     overrides = pkgs: {
       inherit (stdenvLinuxBoot1Pkgs) perl;
       inherit (stdenvLinuxBoot3Pkgs) gettext gnum4 gmp;
@@ -268,8 +267,10 @@ rec {
       '';
 
     initialPath =
-      ((import ../common-path.nix) {pkgs = stdenvLinuxBoot4Pkgs;})
-      ++ [stdenvLinuxBoot4Pkgs.patchelf stdenvLinuxBoot4Pkgs.paxctl ];
+      ((import ../common-path.nix) {pkgs = stdenvLinuxBoot4Pkgs;});
+
+    extraBuildInputs =
+      [ stdenvLinuxBoot4Pkgs.patchelf stdenvLinuxBoot4Pkgs.paxctl ];
 
     gcc = wrapGCC rec {
       inherit (stdenvLinuxBoot4Pkgs) binutils coreutils;
@@ -284,7 +285,7 @@ rec {
     fetchurlBoot = fetchurl;
 
     extraAttrs = {
-      inherit (stdenvLinuxBoot3Pkgs) glibc;
+      glibc = stdenvLinuxGlibc;
       inherit platform bootstrapTools;
       shellPackage = stdenvLinuxBoot4Pkgs.bash;
     };