Staphylococcal colonization was compared in healthy dogs and in dogs with atopic dermatitis. Bacterial swabs were collected from the nasal mucosa, ear and perineum of 43 healthy and 24 atopic dogs and also from potentially infected skin lesions of the atopic dogs. Coagulase positive staphylococcal isolates were identified to the species level. At the time of this study Staphylococcus intermedius was considered a single species but has since been recognized as comprising at least three species with canine isolates believed to belong to Staphylococcus pseudintermedius. Of atopic dogs, 87.5% were colonized with S. intermedius compared to only 37.2% of healthy dogs. The ear was the only carriage site that showed any significant difference in S. intermedius isolation between healthy and atopic dogs. The perineum represented the most frequently colonized mucosal site for both groups. Sampling the nasal mucosa alone identified 71.4% of atopic and 37.5% of healthy S. intermedius carriers. Inclusion of a perineal swab identified 100% of atopic and 93.8% of healthy carriers. S. intermedius was isolated from all the lesional sites sampled from atopic dogs. Significantly fewer dogs were colonized by Staphylococcus aureus than S. intermedius, and there was no significant difference between S. aureus colonization of atopic and healthy dogs. S. aureus was not recovered from any lesions in atopic dogs. The results show that S. intermedius carriage is more prevalent in atopic dogs compared to healthy dogs and that to identify staphylococcal carriers both the nasal mucosa and the perineum should be sampled.