Background Exposure to microbial cell wall agents (MCWAs) has been related to the risk for atopy, otitis, and rhinitis. Objectives To relate domestic exposure to two important MCWAs-b-glucan and endotoxin-to the risk for otitis, rhinitis, atopy, and allergy in a sample of children from Singapore. Methods Subjects (n = 98) were recruited from July 2006 to December 2008. Blood samples were taken to determine nonspecific IgE and skin prick tests were performed. Dust samples were collected from the bedrooms of the subjects and analyzed for the content of b-glucan and endotoxin, using the Limulus method. Results Levels of IgE were significantly higher among children with rhinitis, and these children also had a larger proportion of atopics. There were no differences in b-glucan values between children with otitis, children with rhinitis, and controls. Endotoxin levels were lower in the homes of children with otitis, with a tendency for the levels to be lower in those with rhinitis. Among children with a high level of b-glucan, there was a higher proportion of those with high IgE values and atopy. Conclusions The results suggest that a low level of endotoxin is a risk factor for otitis and that a high level of b-glucan is a risk factor for atopic sensitisation. Reactions to domestic indoor exposure are determined by several indoor agents and their relative exposure levels.