The brain is the most widely studied body organ, and yet our understanding of its operation and the connection between changes to the physiology and the progression of disease is quite limited. Modern imaging tools, including optical imaging techniques, have enabled the study of many neural diseases and conditions and have assisted in evaluating the effect of drugs in model animal pre-clinical studies and in medical diagnosis. This course will review the principles and major optical techniques used for optical brain imaging. We will review the main cellular types in the brain and the organization of the anatomical regions into functional units. We will compare the major optical techniques used in brain imaging and discuss the contrast mechanisms that are used in each technique.<p> </p> We will review the use of external markers (mainly fluorescent markers), compare them to optical imaging techniques that use intrinsic contrast mechanisms (scattering, absorption, coherence, auto-fluorescence), and give examples in functional imaging of blood flow, oxygen levels, and neuronal activity. New methods using genetic introduction of proteins to control brain activity (Optogenetics) and selectively label cells will be described. Finally, we will discuss, with the help of examples, the relevance of these optical techniques in pre-clinical studies and clinical diagnosis.