The global epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) is characterized by different clonal lineages with different epidemiological behaviour. There are pandemic hospital clones (hospital-associated (HA-)MRSA), clones mainly causing community-acquired infections (community-associated (CA-)MRSA, mainly USA300) and an animal-associated clone (ST398) emerging in European and American livestock with subsequent spread to humans. Nosocomial transmission capacities (RA) of these different MRSA types have never been quantified. Using two large datasets from MRSA outbreaks in Dutch hospitals (dataset 1, the UMC Utrecht for 144 months; dataset 2, 51 hospitals for six months) and a recently developed mathematical model, we determined the genotype-specific RA for ST398 and non-ST398 isolates (categorized as HA-MRSA), using observational data, the detection rate of MRSA carriage and the discharge rate from hospital as the input. After detection of 42 MRSA index cases in dataset 1 (all non-ST398 MRSA) 5076 people were screened, yielding 30 secondary cases. In dataset 2, 75 index cases (51 non-ST398 MRSA and 24 ST398) resulted in 7892 screened individuals and 56 and three secondary cases for non-ST398 MRSA and ST398, respectively. The ratio between discharge and the detection rate was 2.7. RA values (95% confidence interval (CI)) were 0.68 (0.47-0.95) for non-ST398 MRSA in dataset 1, 0.93 (0.71-1.21) for non-ST398 MRSA in dataset 2 and 0.16 (0.04-0.40) for ST398. The RA ratio between non-ST398 MRSA and ST398 was 5.90 (95% CI 2.24-23.81). ST398 is 5.9 times less transmissible than non-ST398 MRSA in Dutch hospitals, which may allow less stringent transmission-control measures for ST398 MRSA. © 2010 The Royal Society.