Visual Studio 2013 has better support for C99, here is an article from MSDN about it http://blogs.msdn.com/b/vcblog/archive/2013/07/19/c99-librar... . But it is not a complete C99 implementation.
The good news is that with VS 2015 you will be able to use Clang for compiling C code, so hopefully a complete C99/C11 implementation on Windows at some point.