Magnetic resonance imaging (MRI) of brain structures and function is uniquely suited to characterize the range of neuroanatomical and physiological changes that characterize the autism phenotype as it develops over time. In this review, we examine the scientific literature in MRI as applied to autism and related areas, over approximately the last decade, discussing findings which have emerged, methodological stumbling blocks which have been identified, and potential future directions. Structural MRI studies have recently begun to elucidate the neurodevelopmental underpinnings and brain-behavior relationships in autism while fMRI studies, building on the wealth of data in normal individuals, are beginning to characterize the underlying neuropsychological deficits of the disorder. Together, these two methods combine to contribute to a better understanding of the neural basis and brain phenotype of this disorder.