The development of canine atopic dermatitis (CAD) may be related to exposure to mite allergens, bacterial endotoxin and/or fungal glucans. In this study, indoor exposure levels of house dust mite allergens, endotoxins and fungal glucans were measured to determine their possible association with CAD. A case-control study including adult Labrador retrievers with (n=28) and without (controls; n=65) CAD was conducted. Dust samples were collected from the living room floor and the bedding and coat of the dog and these were analyzed for house dust mite allergens Der p1 and Der f1, endotoxin and (1→3)-β-d-glucan levels. Dog owners were also required to return a questionnaire regarding their home characteristics. The endotoxin exposure level in the coats of dogs was significantly inversely associated with CAD (odds ratio 0.38; 95% confidence interval 0.15-0.97; P<0.05). No significant difference was found in exposure levels to house dust mite allergens and fungal glucans. The results indicated that endotoxin exposure is inversely associated with CAD, suggesting a protective effect of high indoor endotoxin exposure towards the development of the condition.