Functional magnetic resonance imaging (fMRI) has developed rapidly into a major non-invasive tool for studying the human brain. However, due to a variety of technical difficulties, it has yet to be widely adopted for use in alert, trained non-human primates. Our laboratory has been developing techniques for such fMRI studies. As background, we first consider basic principles of fMRI imaging, experimental design, and post-processing. We discuss appropriate MRI system hardware and components for conducting fMRI studies in alert macaques, and the animal preparation and behavior necessary for optimal experiments. Finally, we consider alternative fMRI techniques using exogenous contrast agents, arterial spin labeling, and more direct measures of neural activation. © 2006 Elsevier Inc. All rights reserved.