Twenty-eight Scottish artisanal farmhouse cheeses were examined in respect of 16 microbial groups of significance for food safety and cheese character development. Microbial populations were diverse and although Escherichia coli O157 and Salmonella spp. were not detected the occurrence of potential foodborne pathogens was confirmed in 86% of the samples analysed. Mycobacterium avium subsp. paratuberculosis was detected in 25% of the cheeses tested and some Staphylococcus aureus and the Bacillus cereus isolates were enterotoxigenic. Resistance to methicillin and vancomycin and other clinically important antibiotics was detected in some S. aureus and Enterococcus strains. The inappropriate labelling of some raw milk cheeses and the consequences of the complexity of the microbial population on isolation media specificity is discussed.