This stratified cross-sectional epidemiological study included 1053 school children aged 13-17 years. All pupils filled in a questionnaire on building-related symptoms and other relevant health aspects. The following exposure measurements were carried out: room temperature, CO2 level, and relative humidity; building characteristics including mold infestation were assessed, and dust was collected from floors, air, and ventilation ducts during a working day. Dust was examined for endotoxin level, and cultivated for viable molds. We did not find a positive association between building-related symptoms and extent of moisture and mold growth in the school buildings. Five of eight building-related symptoms were significantly and positively associated with the concentration of colony forming units of molds in floor dust: eye irritation, throat irritation, headache, concentration problems, and dizziness. After adjusting for different potentially confounding factors in separate analyses of each symptom, the above-mentioned associations between molds in dust and symptoms were still present, except for concentration problems. However, in none of the analyses was mold exposure the strongest covariate, being secondary to either asthma, hay fever, recent airway infection, or psychosocial factors.