Objective: Determine the impact of comorbid brain injury (BI) and cognitive impairment on spinal cord injury (SCI) rehabilitation outcome. Design: Prospective, multiple cohort longitudinal study. Participants: Persons who sustained SCI and a BI (N = 51) and persons who sustained only an SCI (N = 154) during an 18-month prospective enrollment period were assessed and followed during inpatient rehabilitation. Main outcome measurements: Neurocognitive tests, the functional independence measure (FIM), length of stay (LOS), and Life Satisfaction scales were administered. Results: Persons with an SCI and comorbid BI (Dual Diagnosis [DD]) had significantly lower cognitive scores on the FIM and neurocognitive measures relative to peers with only a spinal cord injury. Persons with DD also had lower Motor FIM scores at discharge despite equal Motor FIM scores at admission to rehabilitation. LOS was significantly longer for DD persons. Conclusions: Preliminary analyses indicate that a comorbid brain injury has a deleterious effect on outcome during rehabilitation for SCI. Persons with a comorbid brain injury have less optimal cognitive and motor skills at discharge and they require a longer length of stay to achieve suboptimal functional gains. The impact of preinjury cognitive dysfunction and types of neuropsychological impairment secondary to acquired brain injury requires further elaboration. Persons with DD may require specialized treatment above any beyond what is currently available.