Methicillin-resistant Staphylococcus aureus (MRSA) is an emerging equine pathogen. To attempt to control nosocomial and zoonotic transmission, an MRSA screening program was established for all horses admitted to the Ontario Veterinary College Veterinary Teaching Hospital, whereby nasal screening swabs were collected at admission, weekly during hospitalization, and at discharge. MRSA was isolated from 120 (5.3%) of 2,283 horses: 61 (50.8%) at the time of admission, 53 (44.2%) during hospitalization, and 6 from which the origin was unclear because an admission swab had not been collected. Clinical infections attributable to MRSA were present or developed in 14 (11.7%) of 120 horses. The overall rate of community-associated colonization was 27 per 1,000 admissions. Horses colonized at admission were more likely to develop clinical MRSA infection than those not colonized at admission (OR 38.9, 95% CI 9.49 160, P < 0.0001). The overall nosocomial MRSA colonization incidence rate was 23 per 1,000 admissions. The incidence rate of nosocomial MRSA infection was at the rate of 1.8 per 1,000 admissions, with an incidence density of 0.88 per 1,000 patient days. Administration of ceftiofur or aminoglycosides during hospitalization was the only risk factor associated with nosocomial MRSA colonization. MRSA screening of horses admitted to a veterinary hospital was useful for identification of community-associated and nosocomial colonization and infection, and for monitoring of infection control practices.