Functional magnetic resonance imaging (fMRI) methods have been extensively applied to study the human brain and its functional organization in healthy and disease states. A strong rationale exists for the extension of this approach to animal models as a translational tool to bridge clinical and preclinical research. Specifically, the development of pharmacological MRI (phMRI), i.e., the use of fMRI to map spatiotemporal patterns of brain activity induced by pharmacological agents, has provided a robust and flexible tool to resolve brain circuits and mechanism-specific functional changes produced by selective intervention in different neurotransmitter systems in vivo. This chapter describes the methodological aspects of fMRI and phMRI in preclinical species, and some of the key findings, with a special emphasis on the translational potential of these methods in neuropharmacological research.