Aim: The aim of this project was to study the age and sex specific occurrence of atopic and non-atopic asthma and other atopic manifestations in a nationwide sample of Swedish pre-school children. Methods: All 70 allergen avoidance day-care centres (AADC) with 84 sections and 140 matched ordinary day-care centres with 440 sections in 62 municipalities across Sweden were sampled. In 2000 the staff at each section responded to a questionnaire on indoor and outdoor environment at the section. In 2002 parents of 5,886 children attending the AADCs and ODCs responded to a postal questionnaire regarding symptoms indicating prevalent asthma, allergic rhinitis, eczema, and food, furred pet and pollen allergy and other data in their children. In 2007, parents of 4255 children responded to an almost identical follow-up questionnaire. Results: The AADCs had far more strict rules than ODCs on furred pets and smoking at home and on perfume use, and the indoor environment was better, owing to better cleaning. The age specific asthma prevalence was curvilinear with a peak at age 3 of 11.4% among boys and 9.8% among girls. In addition the prevalence increased by municipality population density, a proxy for degree of urbanisation. There was a highly significant co-occurrence between all asthma-atopic manifestations, but there was no evidence of ordered sequence of manifestation onset. The asthma incidence was highly dependent on presence or absence of co-occurrence variables. Given the variable mix in the present study population, the annual asthma incidence ranged from 0.6% to 1.2%. Conclusions: AADCs had more strict rules and a better indoor environment than ODCs. The asthma prevalence was affected by age, sex and degree of urbanisation. There was close co-occurrence between all asthma and atopic manifestations but no evidence of ordered sequence of onsets. The annual asthma incidence was strongly dependent of co-occurrence conditions.