We investigated the association of bacille Calmette-Guérin (BCG) vaccination and atopic manifestations among children. Because many children in the study area were from minority ethnic groups, the effect of ethnicity on disease prevalence was also analyzed. A mandatory health survey included all preschool children from Berlin in 1994. Trained medical personnel asked parents whether their child had ever had a diagnosis of atopic dermatitis (AD), bronchial asthma (BA), and hay fever (HF) or symptoms suggestive of these conditions. BCG-vaccination status was recorded from official vaccination documents. Ethnicity of the child was defined by maternal citizenship. We included 38 808 children in our study (20 813 children from former west Berlin), on average aged 6 years. The proportion of children with a foreign family background was 2.1% in East Berlin and 27.5% in West Berlin. BCG vaccination was more common in East Berlin than in West Berlin (94.2% vs. 16.5%) and in West Berlin more common among children with a foreign family background compared with Germans (25.3% vs. 13.2%). The adjusted odds ratio (95% CI) for BA was 0.85 (0.71–1.00) for BCG-vaccinated individuals. BCG vaccination was not significantly associated with AD or HF. Among non-German children, the odds ratios were 0.35 (0.30–0.42) for AD, 0.58 (0.48–0.70) for BA, and 0.72 (0.54–0.92) for HF. The OR for AD among children living in eastern Berlin was 1.19 (1.04–1.36), no significant regional differences were found for BA or HF. This study demonstrated a weak protective effect of BCG vaccination against asthma but a much stronger protective effect of non-German ethnicity against atopic manifestations among preschool children from Germany.