Non-invasive imaging technologies play a substantial role in the evaluation of physiological and pathophysiological processes. They are indispensable in biomedical research and in the clinic. In the past decade, designated small animal imaging scanners have become available for almost all imaging modalities used in clinical routine. These include nuclear imaging techniques such as positron emission tomography (PET) or single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), X-ray computed tomography (CT), and ultrasound (US). Among the imaging modalities used for small animal imaging, optical techniques such as fluorescence imaging (FI) and biolumnescence imaging (BLI) are becoming increasingly important. In this chapter, we describe the basic principles of optical imaging and the application of the techniques for the non-invasive visualization of biological processes in animal disease models, with special emphasis on small animal models of stroke.