The study aim was to compare the prevalence of asthma, rhinitis and eczema in children living in Munster, western Germany, and Greifswald, eastern Germany, and to investigate associations of several characteristics and exposures with atopic disease symptoms. In 1994 and 1995, questionnaire information was gathered on 5-8 yr old children (n=3,741 in Munster and n=2,857 in Greifswald) and 12-15 yr olds (n=4,003 and n= 3,153, respectively) using the phase I protocol of the International Study of Asthma and Allergies in Childhood (ISAAC). The 12 month period prevalences of reported atopic disease symptoms in 5-8 yr olds were generally higher in Munster than in Greifswald, whereas only a few prevalence differences were observed in 12-15 yr olds. In both age groups the reported lifetime prevalences of asthma, hay fever and eczema were lower in Greifswald. Indoor exposures such as wood or coal heating and feather bedding were negatively associated with symptoms, whereas exposures such as truck traffic in a residential street or active smoking were positively associated with symptoms. Wood or coal heating could partly explain the prevalence difference of allergic rhinitis symptoms among 5-8 yr olds between Munster and Greifswald. The findings provide additional evidence for a role of several characteristics and exposures as potential determinants of asthma and allergies in children.