The role of immunization in the development of atopic disorders is still under debate. One reason might be, that because of high vaccination coverage in most countries only few and selected children are not immunized, leading to unstable and often biased effect estimates. In Germany, the situation was different between 1985 and 1991: bacillus Calmette-Guérin (BCG) and pertussis vaccination were not officially recommended leading to high numbers of non-vaccinated children in the 1990s. We report on a cross-sectional study with 1673 participants among 5- to 7-year-old preschool children conducted in 1996. We found no hint that BCG vaccination or whole-cell pertussis (WCP) vaccination may lead to higher prevalences of asthma, allergic rhinitis, eczema or allergic sensitization at preschool age. None of the associations was significantly positive. WCP vaccination may be protective against asthma OR 0.55 (95% CI: 0.31–0.98) and against symptoms of eczema in boys.