A study was performed at the four sentinel health departments of Baden-Württemberg between November 1999 and March 2000 to investigate the indoor levels of fungi at the homes of school children (mean age 10 y) and to describe possible associations with allergy statuses. Three hundred and ninety-seven households of school children with (n = 199) and without (n = 198) allergic history were included in the study. The median of colony forming units (CFU/m3) of fungi, measured in the children's bedrooms' in indoor air, was 105 (range 5 to 15,000), in outdoor air 110 (range 10 to 1500). The median of viable mould spores (CFU/g dust) in floor dust was 28,500 (range 1500 to 1,235,000), in mattresses 16,250 (range 0 to 2,500,000). Neither climatological conditions, nor differences between urban and rural regions showed a systematic influence on fungi counts. There was no difference in concentrations and distribution of fungi species levels between children with and without allergic history. The sensitization rate against molds (IgE) was higher for children with allergic condition (9.2%) than in control children (4.4%), but there was no association with the fungi counts in the rooms. In conclusion, the study defined the mould levels in children's rooms, but did not find an association with allergic history of the children or their sensitization rate.