The study examined the exposure to biological indoor air agents and their possible role for allergies and respiratory tract illnesses of children. It was conducted as a case control study (atopic vs non-atopic children) at the four surveillance public health departments in Baden-Württemberg in the winter season 1999/2000 and included 379 children of the fourth class. The concentrations of the house dust mite antigens Der F1, Der p1, and Der Gr2 as well as cat allergen Fel d1 were determined in the children's bedrooms on the ground and in the mattress. Specific IgE-antibodies against allergens from house dust, mites and cat were determined in the serum of the children. For mite allergens the following medians ( micro g/g) were estimated in floor dust: Der p1 = 0.6, Der f1 = 2.3, Gr2 = 0.1; in mattresses: Der p1 = 1.2, Der f1 = 3.4, Gr2 = 0.3. The median of Fel d1 in floor dust was 0.2 microg/g, in mattresses 0.1 microg/g. Sensitisation to dust mite allergen was found to be more prevalent than sensitisation to cat. The distribution of sensitisation among the cases and controls is different. Among the cases, more subjects were sensitised to dust mites (32.9 %) and cat (13.1 %). Among the controls, 17.1 % were sensitised to dust mites and 4.1 % to cat. The results showed no direct association between the prevalence of allergies or respiratory tract illnesses and the indoor concentrations of the allergens. Possible reasons for these findings are discussed.