It has been hypothesized that a stimulation of regulatory cytokines by microbial compounds reduces autoimmune as well as atopic diseases. Farm-related contact to microbial compounds protects from allergies, but no data on the association between farm contact and type 1 diabetes is available. The aim of this study was to test this association. A case-control study was conducted in five children's hospitals. Regular contact to farm animals and potential confounders were assessed using a postal questionnaire. Eligible subjects were all prevalent cases with type 1 diabetes registered in the hospitals and hospital-based control subjects (response rate 91%). Included were children aged 6-16 years living in rural areas with German nationality (242 case and 224 control subjects). Regular contact to stables (adjusted odds ratio 1.2 [95% CI 0.5-2.7]) was not associated with type 1 diabetes. In addition, regular contact to specific farm animals was not associated with case status. There was a tendency for an inverse relationship between allergic rhinitis and type 1 diabetes (0.6 [0.3-1.1]; P = 0.11). There was no evidence that early exposure to farm animals largely decreases the risk in children for developing type 1 diabetes.