We assessed the prevalence of carriage of methicillin-resistant Staphylococcus aureus (MRSA) in anterior nares and stools, and of third-generation cephalosporin resistant enterobacteriaceae and non-fermenting Gram-negative bacilli (RE/RNF) in stools of 748 hospitalized long-stay cirrhotic patients. We also evaluated the consequences of carriage on the epidemiology of hospital-acquired spontaneous bacterial peritonitis, bacteraemia and urinary tract infection (UTI) in these patients. The prevalence of carriage of MRSA and RE/RNF was 16·7% and 14·7% respectively. Whereas RE/RNF carriage did not lead to an increased risk of infection due to RE/RNF, the overall risk of infections caused by MRSA was more than tenfold higher in MRSA carriers. MRSA and RE/RNF carriers had received prior antibiotic therapy to a greater extent than non-carriers (P < 0·001) and MRSA carriers had received prior norfloxacin prophylaxis to a greater extent than the two other groups (P < 0·02). The mortality rate during hospital stay was higher in MRSA and RE/RNF carriers than in non-carriers (P < 0·001). Pugh score (P < 0·0001), age (P < 0·0001), MRSA carriage (P = 0·0018) and bacteraemia (P = 0·0017) were associated independently with mortality. MRSA carriage in hospitalized cirrhotic patients leads to the emergence of infections due to this strain, mainly SBP and bacteraemia. Prior antibiotic therapy and norfloxacin prophylaxis increase the risk of carriage of MRSA.