Traditional flow cytometry methods have been remarkably successful at detecting and sorting specific cells in a sample consisting of many cell types. However, a significant limitation of these methods is their inability to be applied in-vivo. Our research focuses on creating and perfecting novel flow cytometry methods which resolve this problem. Previous work includes the development of a two-photon in-vivo flow cytometry system. The use of multiphoton excitation creates an extremely narrow excitation region, making it possible to record signals from single cells as they propagate through the bloodstream. This eliminates the complicated fluid dynamics required for conventional flow cytometry, and also allows the user to focus on a single blood vessel in a living animal. Current and future work includes investigations of coherent control and the use of fiber optics for monitoring in the bloodstream itself.