Methicillin-resistant Staphylococcus aureus (MRSA) has long been recognized as an important pathogen in human medicine leading to hospital and community-acquired infections. However, it is now also considered a growing problem in veterinary medicine, although causing little or no disease. Although MRSA has already been detected in livestock including poultry, little is known about the epidemiology of MRSA in broiler and layer chickens. We therefore investigated 372 poultry farms in Belgium. We also compared the isolation method recommended by the European Food Safety Authority using two enrichment steps with an isolation method using only one enrichment step. Isolated MRSA was characterized by means of antimicrobial resistance profiling, spa typing, multi-locus sequence typing, and SCCmec typing. MRSA prevalence was 0.8% using the double broth enrichment method, while using the single broth enrichment method it was 1.8%. Five MRSA strains belonged to the livestock-associated (LA) MRSA ST398 (four with spa type t011 and one with t899), and three to the hospital-acquired MRSA ST239 spa type t037. The ST239 strains carried SCCmec type III while those belonging to ST398 carried SCCmec type IV or V. All isolates showed additional resistance to erythromycin and tetracycline apart from the expected resistance to cefoxitin and penicillin. All strains were susceptible to linezolid, mupirocin and vancomycin. In conclusion, a higher sensitivity for the isolation of LA-MRSA was obtained using only one enrichment step. While the typical LA-MRSA ST398 was present at low prevalence in poultry, human-associated strains have also been found.