How the basal ganglia contribute to the execution of learned motor skills has been thoroughly investigated. The two dominant models that have emerged posit roles for the basal ganglia in action selection and in the modulation of movement vigor. Here we test these models in rats trained to execute highly stereotyped and idiosyncratic task-specific motor sequences. Recordings and manipulations of neural activity in the striatum were not well explained by either model, and suggested that the basal ganglia, in particular its sensorimotor arm, are crucial for controlling the detailed kinematic structure of the learned behaviors. Importantly, the neural representations in the striatum, and the control functions they subserve, did not depend on the motor cortex. Taken together, these results extend our understanding of basal ganglia function, by suggesting that they can control and modulate lower-level subcortical motor circuits on a moment-by-moment basis to generate stereotyped learned motor sequences.