diff --git a/config/compiler/BUILD.gn b/config/compiler/BUILD.gn
index dde34c1ea..60954b3dc 100644
--- a/config/compiler/BUILD.gn
+++ b/config/compiler/BUILD.gn
@@ -307,15 +307,6 @@ config("compiler") {
     cflags += [ "-fcolor-diagnostics" ]
   }
 
-  # Makes builds independent of absolute file path.
-  # clang-cl (used if is_win) doesn't expose this flag.
-  # Currently disabled for nacl since its toolchain lacks this flag (too old).
-  # TODO(zforman): Once nacl's toolchain is updated, remove check.
-  if (is_clang && !is_win && !is_nacl) {
-    absolute_path = rebase_path("//.")
-    cflags += [ "-fdebug-prefix-map=$absolute_path=." ]
-  }
-
   # C++11 compiler flags setup.
   # ---------------------------
   if (is_linux || is_android || (is_nacl && is_clang)) {
diff --git a/config/linux/pkg_config.gni b/config/linux/pkg_config.gni
index 9ab1de97a..58769e269 100644
--- a/config/linux/pkg_config.gni
+++ b/config/linux/pkg_config.gni
@@ -52,7 +52,7 @@ if (sysroot != "") {
   # Pass the sysroot if we're using one (it requires the CPU arch also).
   pkg_config_args = [
     "-s",
-    rebase_path(sysroot),
+    sysroot,
     "-a",
     current_cpu,
     "--system_libdir",
diff --git a/config/posix/BUILD.gn b/config/posix/BUILD.gn
index 1abbcebba..6f65443d7 100644
--- a/config/posix/BUILD.gn
+++ b/config/posix/BUILD.gn
@@ -13,7 +13,7 @@ assert(is_posix)
 config("runtime_library") {
   if (!is_mac && sysroot != "") {
     # Pass the sysroot to all C compiler variants, the assembler, and linker.
-    cflags = [ "--sysroot=" + rebase_path(sysroot, root_build_dir) ]
+    cflags = [ "--sysroot=" + sysroot ]
     asmflags = cflags
     ldflags = cflags
 
diff --git a/config/sysroot.gni b/config/sysroot.gni
index dcd215a34..29a2b6117 100644
--- a/config/sysroot.gni
+++ b/config/sysroot.gni
@@ -19,17 +19,17 @@ if (current_toolchain == default_toolchain && target_sysroot != "") {
 } else if (is_android) {
   import("//build/config/android/config.gni")
   if (current_cpu == "x86") {
-    sysroot = "$android_ndk_root/$x86_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$x86_android_sysroot_subdir")
   } else if (current_cpu == "arm") {
-    sysroot = "$android_ndk_root/$arm_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$arm_android_sysroot_subdir")
   } else if (current_cpu == "mipsel") {
-    sysroot = "$android_ndk_root/$mips_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$mips_android_sysroot_subdir")
   } else if (current_cpu == "x64") {
-    sysroot = "$android_ndk_root/$x86_64_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$x86_64_android_sysroot_subdir")
   } else if (current_cpu == "arm64") {
-    sysroot = "$android_ndk_root/$arm64_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$arm64_android_sysroot_subdir")
   } else if (current_cpu == "mips64") {
-    sysroot = "$android_ndk_root/$mips64_android_sysroot_subdir"
+    sysroot = rebase_path("$android_ndk_root/$mips64_android_sysroot_subdir")
   } else {
     sysroot = ""
   }
@@ -37,13 +37,13 @@ if (current_toolchain == default_toolchain && target_sysroot != "") {
   # By default build against a sysroot image downloaded from Cloud Storage
   # during gclient runhooks.
   if (current_cpu == "x64") {
-    sysroot = "//build/linux/debian_wheezy_amd64-sysroot"
+    sysroot = rebase_path("//build/linux/debian_wheezy_amd64-sysroot")
   } else if (current_cpu == "x86") {
-    sysroot = "//build/linux/debian_wheezy_i386-sysroot"
+    sysroot = rebase_path("//build/linux/debian_wheezy_i386-sysroot")
   } else if (current_cpu == "mipsel") {
-    sysroot = "//build/linux/debian_wheezy_mips-sysroot"
+    sysroot = rebase_path("//build/linux/debian_wheezy_mips-sysroot")
   } else if (current_cpu == "arm") {
-    sysroot = "//build/linux/debian_wheezy_arm-sysroot"
+    sysroot = rebase_path("//build/linux/debian_wheezy_arm-sysroot")
   } else {
     # Any other builds don't use a sysroot.
     sysroot = ""
@@ -63,9 +63,7 @@ if (current_toolchain == default_toolchain && target_sysroot != "") {
       _script_arch = "amd64"
     }
     assert(
-        exec_script("//build/dir_exists.py",
-                    [ rebase_path(sysroot) ],
-                    "string") == "True",
+        exec_script("//build/dir_exists.py", [ sysroot ], "string") == "True",
         "Missing sysroot ($sysroot). To fix, run: build/linux/sysroot_scripts/install-sysroot.py --arch=$_script_arch")
   }
 } else if (is_mac) {