Currently, there is ongoing discussion regarding potential protective effects of exposure to pets during early childhood on the development of atopic disorders in children later in life. We used data from three consecutive cross-sectional surveys to study the relationship between contact with dogs, cats and other pets, and allergic diseases in schoolchildren 5–14 years of age. In three study areas of the former East Germany, 7,611 questionnaires were received from 5,360 different children who were examined between 1992 and 1999 as school entrants, or third- or sixth-graders. Allergic sensitization to common aeroallergens (birch, grass, mite, cat) was assessed by specific serum immunoglobulin E (IgE) concentrations [using radioallergosorbent testing (RAST)] for 85% of the children. After adjustment for possible confounders, inverse associations were found between contact with dogs in the first year of life and lifetime prevalences of asthma [odds ratio (OR) = 0.68; 95% confidence interval (CI): 0.43–1.08], hay fever (OR = 0.61; 95% CI: 0.39–0.95), eczema (OR = 0.76; 95% CI: 0.61–0.94), itchy rash (OR = 0.76; 95% CI: 0.61–0.94), and pollen sensitization (RAST ≥ 4: OR = 0.56; 95% CI: 0.38–0.82). These effects were more pronounced for children with atopic parents. Similar associations were observed for current contact with dogs. We identified no clear relationships for the other pets (cats, rodents, birds), with the exception that children currently exposed to cats were more likely to be sensitized against cats. In conclusion, this study supports the hypothesis of a potential protective mechanism related to dog exposure in early life, especially for children of atopic parents. However, this association was found only for dogs and not for cats.