BACKGROUND Tobacco smoke, containing more than 4800 chemical substances with a large number of mutagenic and carcinogenic compounds, is the most important indoor pollution. Aim of the study was to analyse the relationship between exposure of children (2-15 years) to environmental tobacco smoke (ETS) with the amount of respiratory diseases, the occurrence of atopic diseases and the risk for genotoxic damage. METHODS Within the last 1.5 years 216 children were included in the study. Smoking habits of the family, environmental settings, housing, nutrition, social and economic factors were assessed by a detailed questionnaire. Two different effect markers were used to assess molecular and genetic damage. Biochemical effect of ETS was quantified by 4-aminobiphenyl-hemoglobin (4-ABP-Hb) adducts and the genotoxic damage was determined by chromosomal damage as seen in the micro nucleus test in lymphocytes. RESULTS Chronic rhinosinusitis and allergic rhinitis are accumulated in the ETS-exposed children. In the ETS-group atopic diseases (allergic rhinitis, extrinsic asthma or neurodermatitis) were significantly more frequent (39.5 %, p = 0.01) than in the non-exposed group (23 %). In addition the genetic predisposition was significantly decreased in the ETS-group (20.8 %, p = 0.048) compared to the non-exposed group (45 %). Until now, blood samples of 63 individuals were analysed for Hb adducts and 92 for micro nuclei. Hemoglobin adducts of 4-ABP, a human carcinogenic aromatic amine, were significantly elevated in children with smoking parents (mean: 82.2pg/g Hb, p = 0.003) compared to children with non-smoking parents (mean: 60.6 pg/g Hb). ETS-exposed children showed significantly higher micro nucleus frequencies (mean ETS: 8.0/1000 binucleate (BN) cells, p = 0.001) than non-ETS exposed children (mean: 6.2/1000 BN cells). CONCLUSIONS Our data underline the thesis, that ETS plays an important role for the development of atopic diseases. The significantly increased effect markers of tobacco smoke in exposed children give evidence, that ETS causes elevated molecular and genotoxic damage in children.