Background: The indoor home environment has been shown to be associated with the presence of respiratory symptoms and atopic disease. Methods: Two cross-sectional surveys (1995–2000) were conducted, using data from the ISAAC phase I and III surveys, collected in Münster, Germany (n = 6,996, response 81.8%). We analyzed the prevalence ratio (PR) for several indoor exposures and asthma-related outcomes in 6- to 7-year-old children, adjusting for potential confounders. Results: Positive associations were observed regarding exposure to molds, environmental tobacco smoke, cooking with gas and space heating with fossil fuels, but most associations were not statistically significant. Surprisingly, presence of a carpet was negatively associated with most respiratory conditions. When restricting the analysis to participants without avoidance of a carpet due to a history of atopic disease, the protective associations disappeared. Mostly, present pet ownership did not show positive associations with respiratory symptoms. However, ownership at different times in life revealed positive associations, particularly in regard to birds owned in the first year of life (PR 1.51, 95% CI 1.11–2.06, for sleep disturbance due to wheeze and PR 1.28, 95% CI 1.01–1.63, for wheeze during the last 12 months, respectively). Conclusions: Only few indoor factors were positively associated with the studied outcomes. The change of associations in participants that reported allergy-related avoidance of carpets suggests that the observed effects are a result of asthmatics’ changed behavior. The effect of allergy-related change in behavior and the results observed concerning the ownership of pets at different ages underline the need of establishing a precise temporal relationship between disease and exposure.

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