Two thousand seven hundred eighty single-patient, methicillin-resistant Staphylococcus aureus (MRSA) isolates collected between January 1995 and December 1999 at 17 tertiary care hospital sites across Canada were characterized by phenotypic and genotypic techniques. Six clonal types, as defined by pulsed-field gel electrophoresis, comprised 87% of all isolates and were labeled Canadian (C) MRSA-1 through -6. CMRSA-1 was the most prevalent clonal type, representing 45% of all MRSA. CMRSA-2 was indistinguishable from the New York clone and was more likely to be associated with community acquisition. CMRSA-3 was more likely to cause an infection, compared with the other CMRSA types. CMRSA-4 was indistinguishable from epidemic (E) MRSA-16 from the United Kingdom. Both CMRSA-5 and -6 occurred primarily in single-site, multiyear outbreaks. This study confirms that the epidemiology of MRSA in Canada is evolving, but most isolates at this time appear to belong to one of a small number of epidemic clones.