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Background: Exposure to endotoxin and allergens in house dust has been found to be associated with childhood wheeze and asthma. Neonatal lung function is rarely examined in relation to this exposure., Objectives: To assess the association between exposure to endotoxin, house dust mite and cat allergens and neonatal lung function, and respiratory symptoms and eczema in infancy., Methods: In the Wheezing Illnesses Study Leidsche Rijn (WHISTLER) birth cohort study, levels of endotoxin, house dust mite allergens, and cat allergen have been measured in dust samples collected in the child's home. Lung function was measured before age 2 months, and respiratory symptoms and eczema were recorded in a daily diary during the first year of life. Associations of lung function (N = 302), respiratory symptoms (N = 361), and eczema (N = 342) with endotoxin and allergen levels have been studied by means of linear and logistic regression, respectively., Results: Mattress dust endotoxin was associated with a significant increase in neonatal respiratory compliance [adjusted mean difference (95% confidence interval) 2.31 (0.33; 4.29) ml/kPa per interquartile range increase in exposure] and a non-significant decrease in neonatal airway resistance [0.32 (-0.77; 0.14) kPa/l/s]. There were no associations between allergen exposure and neonatal lung function and respiratory symptoms., Conclusions: Environmental exposure to endotoxin may have an important role in the development of lung function., (© 2012 John Wiley & Sons A/S.)