This study addressed whether whole cell pertussis-vaccinated children have a different risk of atopic disorders compared with children who did not receive this vaccination. Data on vaccination status, atopic disorders and child and family characteristics of the children of 700 families were collected in this retrospective study. A minority of these 700 families refused vaccinations for religious reasons. The relation between pertussis-vaccination status and atopic disorders was analysed by means of adjusted logistic regression for repeated measurements in order to account for the correlation between sibship members. The 700 families included 1,961 children. Data on vaccination status and atopic disorders were available for 1,724 children. Vaccinated children had a reduced risk of atopic disorders. Whole cell pertussis vaccination is associated with a lower risk of atopic disorders, though other vaccine components (diphtheria, tetanus, poliomyelitis) or other vaccinations may also be involved.