Medical conditions co-occurring with traumatic brain injury (TBI) are associated with outcomes, and comorbidity indices such as Charlson and Elixhauser are used in TBI research, but they are not TBI specific. The purpose of this research was to develop an index or indices of medical conditions, identified in acute care after moderate to severe TBI, that are associated with outcomes at rehabilitation discharge. Using the TBI Model Systems National Database, the International Classification of Diseases, Ninth Revision (ICD-9) and Tenth Revision (ICD-10) codes of 8988 participants were converted to Healthcare Cost and Utilization Project (HCUP) diagnostic categories. Poisson regression models were built predicting Disability Rating Scale and Functional Independence Measure Cognitive and Motor subscale scores from HCUP categories after controlling for demographic and injury characteristics. Unweighted, weighted, and anchored indices based on the outcome models predicted 7.5–14.3% of the variance in the observed outcomes. When the indices were applied to a new validation sample of 1613 cases, however, only 2.6–6.6% of the observed outcomes were predicted. Therefore, no models or indices were recommended for future use, but several study findings are highlighted suggesting the importance and the potential for future research in this area.