Background: Household endotoxin exposure in allergy and asthma has been gaining attention for its dual potential to exacerbate these conditions in individuals with established disease and to abrogate atopy before disease onset. Objective: We sought to better understand the home environmental and lifestyle factors influencing house dust endotoxin levels. Methods: From the homes of 86 infants with wheeze in metropolitan Denver, Colorado, house dust endotoxin (detected with a standardized Limulus Amebocyte Lysate assay) and common indoor allergen (Fel d 1, Can f 1, Der p 1, Der f 1, and Bla g 1) contents were quantified. Comprehensive home environment and lifestyle questionnaires were completed during home visits by trained study staff and parents. Results: House dust endotoxin levels were associated with only 2 home environmental features: animals in the home and the presence of central air conditioning. The strongest positive associations were found with animals in the home. Interestingly, the homes without cats or other animals revealed a negative correlation between house dust Fel d 1 and endotoxin (P = .03). Central air conditioning, especially during months of typical use, was associated with lower house dust endotoxin levels. No significant associations between house dust endotoxin levels and home dampness, number of household inhabitants or young children, cleaning frequency, or presence of tobacco smokers in the home were found. Conclusions: Indoor endotoxin exposure can be increased by the presence of animals in the home and decreased with central air conditioning. In some homes without animals, where allergen exposure adequate for sensitization still occurs, there are lower levels of house dust endotoxin. Therefore in homes without animals, factors that influence allergen and endotoxin levels in house dust probably differ. Households with detectable allergen levels but low endotoxin levels may provide a predisposing environment for animal allergen sensitization.