Synchronizing movements with auditory beats, compared to visual flashes, yields divergent activation in timing-related brain areas as well as more stable tapping synchronization. The differences in timing-related brain activation could reflect differences in tapping synchronization stability, rather than differences between modality (i.e., audio-motor vs. visuo-motor integration). In the current fMRI study, participants synchronized their finger taps with four types of visual and auditory pacing sequences: flashes and a moving bar, as well as beeps and a frequency-modulated 'siren'. Behavioral tapping results showed that visuo-motor synchronization improved with moving targets, whereas audio-motor synchronization degraded with frequency-modulated sirens. Consequently, a modality difference in synchronization occurred between the discrete beeps and flashes, but not between the novel continuous siren and moving bar. Imaging results showed that activation in the putamen, a key timing area, paralleled the behavioral results: putamen activation was highest for beeps, intermediate for the continuous siren and moving bar, and was lowest for the flashes. Putamen activation differed between modalities for beeps and flashes, but not for the novel moving bar and siren. By dissociating synchronization performance from modality, we show that activation in the basal ganglia is associated with sensorimotor synchronization stability rather than modality-specificity in this task. Synchronization stability is apparently contingent upon the modality's processing affinity: discrete auditory and moving visual signals are modality appropriate, and can be encoded reliably for integration with the motor system.