Indoor allergens and microbial bio-contaminants play a significant role in asthma symptoms. The aim of the study was to determine levels of house dust mite allergens, bacterial endotoxin, and fungal beta-glucan in homes of 120 asthmatic children in central Taiwan. Dust samples from 120 mattresses (67 double-sided) were analyzed for house dust mite allergens (Der p 1, Der f 1, and Blo t 5), endotoxin, and beta-glucan. Pillows (n = 118) were analyzed for house dust mite allergens only. Kitchen dust samples were analyzed for the cockroach allergen, Bla g 1. Blo t 5 was detected in 9.3% pillows and 82.2% mattresses, Der p 1 in 95.8% pillows and 93.2% mattresses, and Der f 1 in 82.2% pillows and 83.1% mattresses. Geometric mean levels (95% confidence interval) of endotoxin and beta-glucan in mattresses were 108.4 Eu/mg (81.4-144.2) and 25.2 microg/g (22.7-28.0), respectively. House dust mite allergens and endotoxin levels were significantly lower on the bamboo side of 67 mattresses, compared to the inner sprung mattress side. Geometric mean of kitchen Bla g 1 was 0.61 U/g (95% CI: 0.43-0.85). Given the presence of Der p 1, Der f 1 and Blo t 5 in central Taiwan, it is advised to measure allergens of all three house dust mite species to obtain a true index of allergen exposure. Bamboo sides of mattresses had significantly lower house dust mite allergens and endotoxin levels.