This study was carried out to evaluate the relationship between wheezing or sensitization and concentrations of mites, cat and dog allergens, and bacterial endotoxin in Palestine. A nested case-control involved analysis of mattress and floor dust from a 110 children's houses with reported wheezing and without wheezing. We found no consistent associations between allergen levels and either wheeze or specific atopic sensitization. Furthermore, no clear associations between mattress endotoxin levels and wheeze or atopy were found. Endotoxin in floor dust was inversely associated with atopic sensitization and wheeze, statistically significant only for atopic wheeze. Finally, a nonsignificant inverse association was observed between living room endotoxin and atopy within the non-wheezing control group. In conclusion, although our study found mostly negative results, it does suggest that endotoxin on living room floors might protect against atopic wheeze. However, this finding should be interpreted with caution due the relatively small sample size of the study and requires further confirmation.