In the German Health Interview and Examination Survey for Children and Adolescents (KiGGS) from 2003-2006 information was collected on allergic diseases (asthma, atopic dermatitis, hay fever, allergic contact eczema) from a population-based sample of 17,641 0-to 17-year-olds, and blood samples were studied for specific IgE antibodies to 20 common allergens. The lifetime prevalence (LTP) of at least one atopic disease was 22.9 % (95 % CI: 22.0-23.7 %), the 12-month prevalence (12MP) was 16.1 % (15.4-16.8 %); boys (17.3; 16.3-18.2 %) were more frequently affected than girls (14.9; 14.0-15.8 %). Children with a background of migration were less often currently affected by an atopic disease, as were children from families of low social status. According to parents' accounts, the LTP of allergic contact eczema was 9.9 % (9.4-10.5 %); girls (13.8;12.9-14.8) were more frequently affected than boys (6.2; 5.6-6.9 %). Of the 3- to 17-year-olds, 40.8 % (39.6-42.0 %) were sensitised to at least one of the allergens tested; boys (45.0; 43.5-46.5 %) more frequently so than girls (36.4; 35.0-37.9 %). In the states of the former FRG, the LTP of allergic contact eczema was higher (10.2; 9.6-10.9 %) than those in the former GDR (8.4 % 7.4-9.6 %); otherwise there were no East-West differences. The KiGGS data provide the first nationally representative data on allergic diseases and sensitisation. The differences in prevalence observed correspond to a great extent with previous studies and may support the hygiene hypothesis. The prevalences in East and West Germany now seem to have equalised.