The performance of chromogenic media for the detection of methicillin-resistant Staphylococcus aureus (MRSA) in humans, has been evaluated in numerous studies. However, few comparative studies have been performed for the detection of MRSA in pigs. In this study two different salt concentrations (2.5% or 7.5% NaCl) were evaluated in the enrichment nutrient broth and three selective chromogenic media (chromID MRSA, BrillianceMRSA and MRSASelect) for their ability to detect MRSA in swabs from 29 pigs obtained from three different anatomical sampling sites (anterior nares, skin behind both ears and perineum). ChromID MRSA showed the highest relative sensitivity and specificity after enrichment in 7.5% NaCl, followed by MRSASelect and BrilianceMRSA. For all chromogenic media more MRSA-positive results were obtained for specimens collected from skin behind the ears than for specimens taken from both nares and perineum. The results with regard to the anatomical sampling sites were confirmed in a larger study on three different pig farms involving 60 pigs per farm. Skin behind the ears was the anatomical site with the highest relative sensitivity (91.4%) for MRSA detection compared to perineum and anterior nares, with a relative sensitivity of 76.5% and 75.3%, respectively. An increased relative sensitivity could be achieved when combining two anatomical sites. Sampling of anterior nares and skin behind the ears appeared to be the most sensitive combination with a relative sensitivity of 98.2%. These results show that sampling of only the anterior nares underestimates the real pig MRSA prevalence.