Endotoxins are microbiological agents which ubiquitously exist in an indoor environment, and are believed to be causal agents for a number of diseases. This study investigated the indoor levels and determinants of endotoxins and their impact on asthma and allergy diseases among Swedish pre-school children. House dust samples from 390 homes of 198 case children with asthma and allergy and 202 healthy control children were collected in the Dampness Building and Health (DBH) study. House dust endotoxin levels in the child's bedroom and living rooms ranged from 479-188,000 EU/g dust and from 138-942,000 EU/g dust, respectively. Pet-keeping and agricultural activities were significantly associated with the higher endotoxin concentration levels in indoor dust. Endotoxins in theindoor environment did not associate to asthma and allergy diseases in the children. However, we found an association between endotoxins and the presence of disease symptoms in the sub-group of families without indoor pets.