Objectives Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA), collected from 109 Belgian acute-care hospitals during a national survey in 2008, were investigated for macrolide–lincosamide (ML) resistance with particular emphasis on the analysis of erm (T)-carrying isolates. Methods In total, 314 MRSA and 212 MSSA were collected and characterized by spa typing. The SCC mec type of MRSA was determined. Resistance to ML antibiotics was detected by agar dilution and resistant strains were screened by PCR for erm (A), erm (C) and msr (A). Five ML-resistant MSSA isolates, negative by PCR for the aforementioned genes, were further characterized. Results Half of all MRSA isolates ( n = 157; 50.0%) were resistant to erythromycin and harboured the gene erm (A) ( n = 112), erm (C) ( n = 41), erm (A) + erm (C) ( n = 3) or msr (A) ( n = 1). The erm (A) gene was mainly present in MRSA spa -CC002-ST5-SCC mec II and spa -CC008-ST8-SCC mec IV (where CC stands for clonal complex and ST stands for sequence type); the distribution of erm (C) was more diverse. Thirty-five of the 40 erythromycin-resistant MSSA (18.9%) carried the gene erm (A) ( n = 17), erm (C) ( n = 9) or msr (A) ( n = 9). The remaining five MSSA were ST398-t571 isolates, which exhibited closely related ApaI PFGE patterns, harboured the gene erm (T) in the chromosomal DNA and did not exhibit additional resistances. These isolates were from severe infections in patients, of whom four had no contact and one had only indirect contact with livestock via a family member working in animal husbandry. Conclusions The ML–streptogramin B (‘MLS B ’) resistance genes erm (A) or erm (C) were detected in the majority of ML-resistant MRSA and MSSA isolates. The erm (T) gene was identified in MSSA ST398 isolates from five independent patients who lacked direct contact with livestock.