Atopic diseases became an important health problem in affluent Western societies. To study the prevalence and factors associated with the risk of atopic diseases in Germany, data from the German Health Interview and Examination Survey for Children and Adolescents (KiGGS) were analysed (n = 17,450). Standardized, computer-assisted personal interviews with parents and parent-administered questionnaires provided physician diagnoses of allergic rhinoconjunctivitis, atopic dermatitis and asthma as well as data on demographic characteristics, migration background, birth order, age at the beginning of nursery, atopic diseases of parents, parents' smoking status, parents' occupation, breastfeeding and living environment. The life-time prevalence of atopic dermatitis was 13.2% (95% confidence limit: 12.5-13.9%), 10.7% (10.1-11.3%) for allergic rhinoconjunctivitis and 4.7% (4.3-5.1%) for asthma. At least one atopic disease in parents was the strongest factor associated with atopic diseases in the offspring, with a prevalence ratio of up to 2.6. High and middle socio-economic status (prevalence ratio, 95% confidence limit: 1.28, 1.12-1.46; 1.15, 1.01-1.32) were associated with the risk of atopic dermatitis, whereas a two-sided background of migration reduced the risk (0.76, 0.65-0.88). Factors that reduced the risk of allergic rhinoconjunctivitis were parents working as self-employed farmers (0.48, 0.30-0.76) and older siblings (0.80, 0.71-0.89), whereas the beginning of nursery school at older age was associated with an increased risk in children who were cared for outside the family before school age (1.05, 1.00-1.10). Living in mould-infested rooms (1.64, 1.23-2.19), an urban living environment (1.20, 1.02-1.42) and a smoking mother and/or father (1.20, 1.02-1.40) were associated with the risk of asthma. Our results are in line with the so-called 'hygiene hypothesis', which emphasizes the role of environmental factors in addition to a genetic predisposition in the development of atopic diseases. Research on factors associated with atopic diseases can facilitate decisions on preventive strategies. Further studies are needed to explore trends in prevalence and risk factors for atopic diseases.