After injury to one hemisphere in early development, there is evidence for each hemisphere controlling the impaired forelimb. We tested whether control emanated from the injured hemisphere, via bypass circuit through the brainstem, or via ipsilateral corticospinal tract (CST) connections from the uninjured hemisphere. Using pharmacological inactivation of each motor cortex, we found that control of the forelimb differed strongly between uninjured controls and rats with neonatal injury; uninjured rats had only contralateral control, while rats with neonatal CST injury had control from both the contralateral and ipsilateral motor cortex. In contrast to these results from motor cortex inactivation, the physiology and anatomy results supported only the ipsilateral CST from the uninjured hemisphere as a source of motor control. Microstimulation of the motor cortex in the uninjured hemisphere produced responses from both forepaws while stimulation of the injured hemisphere did not elicit responses from either side. Rats with injury had very strong CST connections to both halves of the spinal cord. Interestingly, each forelimb had a different representation within the uninjured hemisphere, suggesting that one hemisphere can encode separate control of the two forelimbs. On the other hand, there was a lack of plasticity in connections in the injured hemisphere. Finally, the cortical representation of the unimpaired forelimb becomes weaker after injury; there may be a cost to bilateral representation.