Currently available evidence on the excess length of stay (LOS) associated with nosocomial infections is limited by methodology, including time-dependent bias. To determine the excess LOS associated with nosocomial meticillin-resistant Staphylococcus aureus (MRSA) infection and colonisation, 797 MRSA-colonised, 167 MRSA-infected and 13 640 MRSA-negative surgical patients were included in a multistate model. The occurrence of MRSA infection or colonisation was the time-dependent exposure, and discharge or death was the study endpoint. The excess LOS was extracted by computing the Aalen–Johansen estimator of the matrix of transition probabilities. Multivariate Cox regression analysis was used to assess the independent effect of MRSA on excess LOS. MRSA infection prolonged LOS by 14.5 [95% confidence interval (CI): 7.8, 21.3] days compared to uninfected patients, and by 5.9 (95% CI: 0.1, 11.7) days compared to patients only colonised by MRSA. The hazard of discharge was reduced by nosocomial MRSA infection both with respect to MRSA-free patients and MRSA carriers [adjusted hazard ratio (HR): 0.69; 95% CI: 0.59, 0.81; and HR: 0.79; 95% CI: 0.65, 0.95, respectively]. MRSA carriage alone did not decrease the hazard of discharge after adjustment for confounding (HR: 1.00; 95% CI: 0.93, 1.07). Multistate modelling is a promising statistical method to evaluate the health-economic impact of nosocomial antibiotic-resistant infections.