diff --git a/cpp/ycm/.ycm_clang_options.py b/cpp/ycm/.ycm_clang_options.py
index b72f3058..cfa2b011 100644
--- a/cpp/ycm/.ycm_clang_options.py
+++ b/cpp/ycm/.ycm_clang_options.py
@@ -60,19 +60,46 @@ def DirectoryOfThisScript():
   return os.path.dirname( os.path.abspath( __file__ ) )
 
 
-def MakeAbsoluteIfRelativePath( path ):
-  if not path.startswith( '.' ):
-    return path
+def MakeRelativePathsInFlagsAbsolute( flags, working_directory ):
+  if not working_directory:
+    return flags
+  new_flags = []
+  make_next_absolute = False
+  path_flags = [ '-isystem', '-I', '-iquote', '--sysroot=' ]
+  for flag in flags:
+    to_append = flag
 
-  full_path = os.path.join( DirectoryOfThisScript(), path )
-  return os.path.normpath( full_path )
+    if make_next_absolute:
+      make_next_absolute = False
+      if not flag.startswith( '/' ):
+        to_append = os.path.join( working_directory, flag )
+
+    for path_flag in path_flags:
+      if flag == path_flag:
+        make_next_absolute = True
+        break
+
+      if flag.startswith( path_flag ):
+        path = flag[ len( path_flag ): ]
+        to_append = path_flag + os.path.join( working_directory, path )
+        break
+
+    if to_append:
+      new_flags.append( to_append )
+  return new_flags
 
 
 def FlagsForFile( filename ):
   if database:
     # Bear in mind that database.FlagsForFile does NOT return a python list, but
     # a "list-like" StringVec object
-    final_flags = PrepareClangFlags( database.FlagsForFile( filename ) )
+    working_directory = database.CompileCommandWorkingDirectoryForFile(
+        filename )
+    raw_flags = database.FlagsForFile( filename )
+    final_flags = PrepareClangFlags(
+        MakeRelativePathsInFlagsAbsolute( raw_flags,
+                                          working_directory ),
+        filename )
 
     # NOTE: This is just for YouCompleteMe; it's highly likely that your project
     # does NOT need to remove the stdlib flag. DO NOT USE THIS IN YOUR
@@ -82,7 +109,8 @@ def FlagsForFile( filename ):
     except ValueError:
       pass
   else:
-    final_flags = [ MakeAbsoluteIfRelativePath( x ) for x in flags ]
+    relative_to = DirectoryOfThisScript()
+    final_flags = MakeRelativePathsInFlagsAbsolute( flags, relative_to )
 
   return {
     'flags': final_flags,
diff --git a/python/completers/cpp/clang_helpers.py b/python/completers/cpp/clang_helpers.py
index 2b598f0f..7e6b7939 100644
--- a/python/completers/cpp/clang_helpers.py
+++ b/python/completers/cpp/clang_helpers.py
@@ -17,11 +17,12 @@
 # You should have received a copy of the GNU General Public License
 # along with YouCompleteMe.  If not, see <http://www.gnu.org/licenses/>.
 
+import os
 
 # Given an interable object that produces strings (flags for Clang), removes the
 # '-c' and '-o' options that Clang does not like to see when it's producing
 # completions for a file.
-def PrepareClangFlags( flags ):
+def PrepareClangFlags( flags, filename ):
   new_flags = []
   skip = True
   for flag in flags:
@@ -37,5 +38,8 @@ def PrepareClangFlags( flags ):
       skip = True;
       continue
 
+    if flag == filename or os.path.realpath(flag) == filename:
+      continue
+
     new_flags.append( flag )
   return new_flags
diff --git a/python/completers/cpp/flags.py b/python/completers/cpp/flags.py
index 6004e113..631e1d3b 100644
--- a/python/completers/cpp/flags.py
+++ b/python/completers/cpp/flags.py
@@ -39,7 +39,7 @@ class Flags( object ):
     try:
       return self.flags_for_file[ filename ]
     except KeyError:
-      flags_module = self.FlagsModuleForFile( filename )
+      flags_module = self._FlagsModuleForFile( filename )
       if not flags_module:
         return ycm_core.StringVec()
 
@@ -52,7 +52,7 @@ class Flags( object ):
       return sanitized_flags
 
 
-  def FlagsModuleForFile( self, filename ):
+  def _FlagsModuleForFile( self, filename ):
     try:
       return self.flags_module_for_file[ filename ]
     except KeyError: