Enterotoxigenic Staphylococcus aureus frequently contaminate milk and milk products causing food poisoning. Staphylococcus aureus were isolated from bovine, ovine and caprine milk and milk filters from 78 dairy production holdings supplying the farmhouse cheese sector in Ireland, using standard culture methods. Molecular methods were applied to study the distribution of genes encoding staphylococcal enterotoxins and toxic shock syndrome toxin in the collection. Multilocus variable number tandem repeat analysis was used to subtype the collection. One hundred and two Staphylococcus aureus (54 milk filters and 48 bulk milk) were recovered from apparently healthy animals; half of the isolates were toxigenic. Our findings are discussed in light of the risks posed to public health.