Molecular imaging with single photon emission computed tomography (SPECT) and positron emission tomography (PET) has revolutionized neuroscience. The external detection of radioactively labeled tracers allows the quantitative analysis of fundamental physiological processes in living brain of experimental animals, and human subjects. For molecular imaging, particular radioisotopes are incorporated into molecules (tracers) intended to serve as markers for cerebral blood fl ow, blood brain barrier physiology, energy metabolism, neurotransmitter synthesis, and neurotransmitter receptors. These tracers are administered to the subject by inhalation or intravenous injection, and swiftly delivered to brain in the arterial blood. During the processes of partitioning of the tracer across the blood brain barrier and its binding to specifi c molecular targets in brain, decay events are recorded by the tomograph and reconstructed into an image, or source map. After registration of the map to a brain template, the radioactivity concentration is assigned to specifi ed anatomic regions. Especially in PET, temporal changes in the brain concentration of radioactivity can be analyzed according to principles of compartmental analysis, so as to evaluate the step-wise processes of tracer uptake and entrapment in brain. The goal of this endeavour is to extract from the images physiological information about the relatively unperturbed brain, which can inform us about the processes underlying cognition, healthy aging, and diseases of the central nervous system. However the interpretation of PET and SPECT images is subject to caveats dictated by factors such as the limited spatial resolution of the instruments, and the validity of the kinetic analyses, which can only approximate the true complexity of biological processes.