When we listen to rhythm, we often move spontaneously to the beat. This movement may result from processing of the beat by motor areas. Previous studies have shown that several motor areas respond when attending to rhythms. Here we investigate whether specific motor regions respond to beat in rhythm. We predicted that the basal ganglia and supplementary motor area (SMA) would respond in the presence of a regular beat. To establish what rhythm properties induce a beat, we asked subjects to reproduce different types of rhythmic sequences. Improved reproduction was observed for one rhythm type, which had integer ratio relationships between its intervals and regular perceptual accents. A subsequent functional magnetic resonance imaging study found that these rhythms also elicited higher activity in the basal ganglia and SMA. This finding was consistent across different levels of musical training, although musicians showed activation increases unrelated to rhythm type in the premotor cortex, cerebellum, and SMAs (pre-SMA and SMA). We conclude that, in addition to their role in movement production, the basal ganglia and SMAs may mediate beat perception.