Indoor bioaerosols (i.e., bacteria, fungi, endotoxin, and beta-1,3-glucan) were determined in daycare centers, office buildings, and domestic environments in the Taipei area. In addition, we used a questionnaire survey to determine associations between indoor dampness, bioaerosols, and airway inflammation and systemic symptoms. We demonstrated that the median levels of indoor bacteria and fungi were the highest in daycare centers, followed by those in homes and office buildings. Similar patterns were observed for endotoxin and beta-1,3-glucan. The prevalences of airway inflammation and systemic symptoms were higher for females in office buildings than for employees in daycare centers; all symptoms were more prevalent in females than males. With respect to the relationship between bioaerosol exposure and airway inflammation and systemic symptoms, we found a strong association between beta-1,3-glucan and lethargy/fatigue.