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This comparative study investigated differences in functional capacity and functional gains of patients admitted for hospital rehabilitation between 2005 and 2011. Patients were grouped according to broad diagnostic categories: neurological, orthopedic, and deconditioned. Functional capacity (Functional Independence Measure (FIM), gait speed) and functional gains were compared between two 1-year patient cohorts (2005 and 2011) for diagnostic groups. In 2011, more patients were admitted (n = 626 vs. n = 474) with a shorter length of stay (mean difference 9.72 days, 95% confidence interval (CI) 5.26 to 14.18) compared to 2005. Functional capacity of patients at admission was worse in 2011 for all measures (P < 0.05). By hospital rehabilitation discharge, no differences were found between the two cohorts (P > 0.497) except for discharge gait speed; in 2011, patients walked faster (mean difference 0.58 m/s, 95% CI 0.05 to 0.11). Higher FIM gain and FIM efficiency was demonstrated in 2011, but differences between diagnostic groups were evident. Deconditioned patients overall demonstrated less gain and efficiency (F > 3.623, P < 0.028). In summary, improved service efficiencies were demonstrated with improved throughput of patients without compromising functional capacity at hospital rehabilitation discharge. These efficiencies seem to be gained through neurological and orthopedic admissions compared to deconditioned admissions.