Microbial indoor air quality and respiratory symptoms of children were studied in 24 schools with visible moisture and mold problems, and in eight non-damaged schools. School buildings of concrete/brick and wooden construction were included. The indoor environment investigations included technical building inspections for visible moisture signs and microbial sampling using six-stage impactor for viable airborne microbes. Children's health information was collected by questionnaires. The effect of moisture damage on concentrations of fungi was clearly seen in buildings of concrete/brick construction, but not in wooden school buildings. Occurrence of Cladosporium, Aspergillus versicolor, Stachybotrys, and actinobacteria showed some indicator value for moisture damage. Presence of moisture damage in school buildings was a significant risk factor for respiratory symptoms in schoolchildren. Association between moisture damage and respiratory symptoms of children was significant for buildings of concrete/brick construction but not for wooden school buildings. The highest symptom prevalence was found during spring seasons, after a long exposure period in damaged schools. The results emphasize the importance of the building frame as a determinant of exposure and symptoms.