The relationship between early motor status and functional outcome after spinal cord injury (SCI) was evaluated prospectively in 52 quadriplegic and 26 paraplegic patients. Motor status was measured within 72 hours of injury and quantified with the Motor Index Score (MIS). Functional status was evaluated with the Modified Barthel Index (MBI). A senior physical therapist completed the MIS and the MBI when each patient was admitted to the spinal cord intensive care unit and every 30 days during rehabilitation. Early motor function was correlated with average daily improvement in functional status including self-care and mobility (p = .001). The initial MIS strongly correlated with functional status of quadriplegics at admission (p = .001), at 60 days, and at rehabilitation discharge (p = .001). In paraplegics, the overall MBI at admission, after 60 days of rehabilitation, and at discharge was not correlated with early motor function. However, the MIS correlated significantly with the MBI self-care subscore at 60 days and at discharge (p = .01), but not with the mobility subscore. The initial MIS was also significantly correlated to functional status at discharge in patients with complete lesions (p = .001), but was not related to functional status at discharge in patients with incomplete lesions. The MIS appears to be a useful tool in predicting function during rehabilitation, although individual differences in ambulation, particularly for patients with paraplegia, limit the predictive utility of this index.