BackgroundColonization with MRSA is believed to have deteriorating effects on neurological rehabilitation patients because MRSA carriers need to be isolated.MethodsMedical records of neurological early rehabilitation patients (most of them after stroke) admitted to a large rehabilitation facility in Northern Germany in 2010 have been carefully reviewed with respect to MRSA status, outcome variables (functional independence), morbidity, and length of stay (LOS).Results74/569 (13.0%) patients were MRSA positive on admission. MRSA carriers had a significantly longer LOS in early neurological rehabilitation (63.7 (37.1) vs. 25.8 (24.5) days, p < 0.001), worse functional status on admission (Barthel index (BI) 13.6 (9.9) vs. 25.6 (24.1), p < 0.001), worse Glasgow Coma Scale (9.5 (3.2) vs. 12.0 (3.3), p < 0.001), more co-diagnoses (20.5 (5.1) vs. 13.3 (5.5), p < 0.001), and higher Patient Clinical Complexity Levels (PCCL). The outcome was significantly worse among MRSA positive patients (BI 25.5 (21.2) vs. 47.4 (31.0), p < 0.001; Early Rehabilitation Index −47.3 (51.4) vs. -26.0 (35.4), p < 0.001). Isolated patients had slightly less therapy per day (131.6 (16.6) vs. 140.2 (18.7) min/day, p < 0.001), but the overall sum of therapy was significantly larger in the MRSA positive group due to longer LOS.ConclusionsFunctional recovery of MRSA carriers in early neurological rehabilitation is worse than in MRSA negative patients. Poorer outcome is not resulting from isolation (less therapy) but from functional status and higher morbidity on admission.