Comorbidity can affect health-care utilization and outcomes, and the results and interpretation of risk adjustment studies that attempt to predict rehabilitation utilization and outcomes are influenced by the choice of comorbidity measurement. Although the identification of an appropriate measurement has been conducted in some populations and outcomes, this information is currently lacking for the non-traumatic brain injury (nTBI) population in inpatient rehabilitation settings. As such, this is a systematic review protocol to survey the methods used to measure comorbidities in the rehabilitation setting for patients with nTBI.Methods/design: MEDLINE, MEDLINE In-Process, Embase, The Cochrane Database of Systematic Reviews, PsycINFO, and Health and Psychosocial Instruments will be systematically searched using the concepts 'nTBI,' 'comorbidity,' and 'rehabilitation.' Grey matters and the reference list of eligible articles will also be searched. Study selection will be performed independently by two reviewers based on predetermined eligibility criteria through two rounds of screening using, first, the title and abstract, followed by full-text. Extracted information will include study purpose, design, and setting; data source and type; outcomes variables; statistical methods; comorbidity measurement method, rationale, justification, or validation; and results involving comorbidity. The data will be tabulated and narratively synthesized. Meta-analyses will be performed if appropriate.