© 2017 Wolters Kluwer Health, Inc. Objective: To examine differences in patient outcomes across Traumatic Brain Injury Model Systems (TBIMS) rehabilitation centers and factors that influence these differences using hierarchical linear modeling (HLM). Setting: Sixteen TBIMS centers. Participants: A total of 2056 individuals 16 years or older with moderate to severe traumatic brain injury (TBI) who received inpatient rehabilitation. Design: Multicenter observational cohort study using HLM to analyze prospectively collected data. Main Outcome Measures: Functional Independence Measure and Disability Rating Scale total scores at discharge and 1 year post-TBI. Results: Duration of posttraumatic amnesia (PTA) demonstrated a significant inverse relationship with functional outcomes. However, the magnitude of this relationship (change in functional status for each additional day in PTA) varied among centers. Functional status at discharge from rehabilitation and at 1 year post-TBI could be predicted using the slope and intercept of each TBIMS center for the duration of PTA, by comparing it against the average slope and intercept. Conclusions: HLM demonstrated center effect due to variability in the relationship between PTA and functional outcomes of patients. This variability is not accounted for in traditional linear regression modeling. Future studies examining variations in patient outcomes between centers should utilize HLM to measure the impact of additional factors that influence patient rehabilitation functional outcomes.