diff --git a/src/bootstrap/config.rs b/src/bootstrap/config.rs
index 9f6e91c8566..2b1d8e67dd8 100644
--- a/src/bootstrap/config.rs
+++ b/src/bootstrap/config.rs
@@ -358,37 +358,37 @@ macro_rules! check {
                                        .collect();
                 }
                 "CFG_MUSL_ROOT" if value.len() > 0 => {
-                    self.musl_root = Some(PathBuf::from(value));
+                    self.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_MUSL_ROOT_X86_64" if value.len() > 0 => {
                     let target = "x86_64-unknown-linux-musl".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.musl_root = Some(PathBuf::from(value));
+                    target.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_MUSL_ROOT_I686" if value.len() > 0 => {
                     let target = "i686-unknown-linux-musl".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.musl_root = Some(PathBuf::from(value));
+                    target.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_MUSL_ROOT_ARM" if value.len() > 0 => {
                     let target = "arm-unknown-linux-musleabi".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.musl_root = Some(PathBuf::from(value));
+                    target.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_MUSL_ROOT_ARMHF" if value.len() > 0 => {
                     let target = "arm-unknown-linux-musleabihf".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.musl_root = Some(PathBuf::from(value));
+                    target.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_MUSL_ROOT_ARMV7" if value.len() > 0 => {
                     let target = "armv7-unknown-linux-musleabihf".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.musl_root = Some(PathBuf::from(value));
+                    target.musl_root = Some(parse_configure_path(value));
                 }
                 "CFG_DEFAULT_AR" if value.len() > 0 => {
                     self.rustc_default_ar = Some(value.to_string());
@@ -397,7 +397,7 @@ macro_rules! check {
                     self.rustc_default_linker = Some(value.to_string());
                 }
                 "CFG_GDB" if value.len() > 0 => {
-                    self.gdb = Some(PathBuf::from(value));
+                    self.gdb = Some(parse_configure_path(value));
                 }
                 "CFG_RELEASE_CHANNEL" => {
                     self.channel = value.to_string();
@@ -417,40 +417,40 @@ macro_rules! check {
                 "CFG_LLVM_ROOT" if value.len() > 0 => {
                     let target = self.target_config.entry(self.build.clone())
                                      .or_insert(Target::default());
-                    let root = PathBuf::from(value);
+                    let root = parse_configure_path(value);
                     target.llvm_config = Some(push_exe_path(root, &["bin", "llvm-config"]));
                 }
                 "CFG_JEMALLOC_ROOT" if value.len() > 0 => {
                     let target = self.target_config.entry(self.build.clone())
                                      .or_insert(Target::default());
-                    target.jemalloc = Some(PathBuf::from(value));
+                    target.jemalloc = Some(parse_configure_path(value));
                 }
                 "CFG_ARM_LINUX_ANDROIDEABI_NDK" if value.len() > 0 => {
                     let target = "arm-linux-androideabi".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.ndk = Some(PathBuf::from(value));
+                    target.ndk = Some(parse_configure_path(value));
                 }
                 "CFG_ARMV7_LINUX_ANDROIDEABI_NDK" if value.len() > 0 => {
                     let target = "armv7-linux-androideabi".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.ndk = Some(PathBuf::from(value));
+                    target.ndk = Some(parse_configure_path(value));
                 }
                 "CFG_I686_LINUX_ANDROID_NDK" if value.len() > 0 => {
                     let target = "i686-linux-android".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.ndk = Some(PathBuf::from(value));
+                    target.ndk = Some(parse_configure_path(value));
                 }
                 "CFG_AARCH64_LINUX_ANDROID_NDK" if value.len() > 0 => {
                     let target = "aarch64-linux-android".to_string();
                     let target = self.target_config.entry(target)
                                      .or_insert(Target::default());
-                    target.ndk = Some(PathBuf::from(value));
+                    target.ndk = Some(parse_configure_path(value));
                 }
                 "CFG_LOCAL_RUST_ROOT" if value.len() > 0 => {
-                    let path = PathBuf::from(value);
+                    let path = parse_configure_path(value);
                     self.rustc = Some(push_exe_path(path.clone(), &["bin", "rustc"]));
                     self.cargo = Some(push_exe_path(path, &["bin", "cargo"]));
                 }
@@ -460,6 +460,29 @@ macro_rules! check {
     }
 }
 
+#[cfg(not(windows))]
+fn parse_configure_path(path: &str) -> PathBuf {
+    path.into()
+}
+
+#[cfg(windows)]
+fn parse_configure_path(path: &str) -> PathBuf {
+    // on windows, configure produces unix style paths e.g. /c/some/path but we
+    // only want real windows paths
+
+    use build_helper;
+
+    // '/' is invalid in windows paths, so we can detect unix paths by the presence of it
+    if !path.contains('/') {
+        return path.into();
+    }
+
+    let win_path = build_helper::output(Command::new("cygpath").arg("-w").arg(path));
+    let win_path = win_path.trim();
+
+    win_path.into()
+}
+
 fn set<T>(field: &mut T, val: Option<T>) {
     if let Some(v) = val {
         *field = v;