BACKGROUND: We examined the associations of family size and birth order with atopy prevalence in rural Poland at two time periods. METHODS: Two cross-sectional surveys were conducted in the same villages and a small town of lower Silesia at an interval of 9 years. In 2003, 1700 (88% of eligible individuals), and in 2012, 1730 (86%) inhabitants aged 5 years or more completed a questionnaire and had a skin prick test for atopy. RESULTS: There was an inverse association between family size and atopy in the village population in 2003; the prevalence of atopy was the highest for those with no siblings (15.2%) and decreased to 5.4% for those with three and more siblings (OR = 0.22; 0.07-0.66). In contrast, there was little or no such protective effect in the town population where the prevalence of atopy was much higher (7.3% in the villages, 20.0% in the town). Nine years later, the prevalence of atopy had increased in the village to be similar to that in the town (19.6% and 19.9% respectively), and the protective effects of family size and birth order in the villages were much weaker (OR = 0.64; 95% CI 0.33-1.27 for three or more siblings). Both protective effects were strongest among children. CONCLUSIONS: The protective effects of family size and birth order on atopy were much stronger in children than in adults and among those living in a village. They largely disappeared with the steep increase in atopy prevalence at all ages; this followed environmental changes on the village farms.