About the best you can do with the Windows API is QueryPerformanceCounter. You can obtain its resolution with QueryPerformanceFrequency. Depending on the situation, this may be use the CPU's RDTSC instruction, in which case the frequency is basically the clock frequency of the CPU. In other cases, it uses a separate clock with a frequency of 1.024 MHz, so the resolution is basically one microsecond.
C++11 adds a chrono class that may be useful as well -- assuming you're using a compiler that already has it. If your compiler doesn't provide an implementation, Boost Chrono is a reasonable substitute that works with most existing compilers/libraries. Again, there's no guarantee that it'll provide nanosecond resolution, but I'd expect that on Windows it'll probably be a portable wrapper around QPC/QPF, so it'll probably give the same resolution they do, just more portably.
