Objectives A mecA homologue gene, named mecC , has been reported in methicillin-resistant Staphylococcus aureus (MRSA) isolates from humans and from diverse animal species. We investigated the proportion, and the phenotypic and genotypic characteristics, of mecC -carrying MRSA recovered from humans in Belgium. Methods A total of 4869 S. aureus isolates, collected by the National Reference Centre from 2003 to 2012, were retrospectively analysed for the presence of mecC . The mecC -carrying MRSA isolates were tested for phenotypic resistance and the presence of toxin genes. Genotyping was performed using spa typing and multilocus sequence typing. Results Nine S. aureus isolates, mecA negative but cefoxitin resistant (MIC 16–64 mg/L), were found to carry the mecC gene. Among these, eight showed resistance to oxacillin (MIC 4–64 mg/L). These isolates remained fully susceptible to all non-β-lactam antimicrobials. Although the proportion of mecC -carrying MRSA in Belgium was low (<1% per year), mecC -MRSA were assigned to three distinct genetic lineages corresponding to clonal complex (CC) 130, CC49 and CC1943. Conclusions This first Belgian nationwide analysis showed a low occurrence of mecC -MRSA. Further studies should be conducted to better understand the reservoirs and risk factors for mecC -MRSA acquisition.