Good household hygiene practices may improve indoor air quality in the domestic environment. Conversely, a 'hygiene hypothesis' is challenging the importance of hygiene and sanitation at home. This study aims to investigate the relationship between household hygiene practices and dampness at home and current wheezing, asthma and other allergic conditions among Australian children. Nine hundred and ninety-six children from four primary schools in Perth, Western Australia, were recruited for a domestic environmental and health survey during March and April of 2002. The results showed that high cleanliness scores were negatively associated with moulds at home before and after adjustment for age of dwelling (p < 0.001). High ventilation scores were inversely related with damp patches, condensation and moulds at home (p < 0.05). However, households with high cleanliness scores appeared to have significantly higher prevalence of current wheezing (p < 0.05) and current rhino-conjunctivitis (p < 0.05) in children. The association remained even after controlling for confounders such as age and gender of children, asthma history of parents, passive smoking and dampness at home.