BACKGROUND/OBJECTIVE: To test the hypothesis that apolipoprotein E (APOE) polymorphisms are associated with outcomes after spinal cord injury (SCI). METHODS: Retrospective cohort study, from rehabilitation admission to discharge. PARTICIPANTS: Convenience sample of 89 persons with cervical SCI (C3-C8) treated from 1995 through 2003. Median age was 30 years (range 14-70); 67 were male (75%) and 83 were white (93%). MAIN OUTCOME MEASURES: American Spinal Injury Association (ASIA) motor and sensory scores, ASIA Impairment Scale (AIS), time from injury to rehabilitation admission, and length of stay (LOS) in rehabilitation. RESULTS: Subjects with an APOE epsilon4 allele (n = 15; 17%) had significantly less motor recovery during rehabilitation than did individuals without an epsilon4 allele (median 3.0 vs 5.5; P < 0.05) and a longer rehabilitation LOS (median 106 vs 89 days; P = 0.04), but better sensory-pinprick recovery (median 5.0 vs 2.0; P= 0.03). There were no significant differences by APOE epsilon4 allele status in sensory-light touch recovery, likelihood of improving AIS Grade, or time from injury to rehabilitation admission. CONCLUSIONS: APOE epsilon4 allele was associated with differences in neurological recovery and longer rehabilitation LOS. Genetic factors may be among the determinants of outcome after SCI and warrant further study.