Allergic disorders represent a major health problem in most developed countries, but few population-based studies have focused on these disorders in early childhood. The aims of the present study were to investigate the prevalence, gender differences and distribution of allergy related disorders and their association to sensitization among unselected children, 2 yrs of age, in a general population. A population-based study with parental self reported questionnaire data involving allergy related symptoms and results from allergy tests from 4783 two-yr-old children was conducted, and skin prick tests (SPT) of a randomly selected sample comprising 390 children were performed. In the total population the prevalence of reported wheeze was 26%, doctor diagnosed asthma (DDAsthma) 7.0%, atopic dermatitis (AD) 17% and allergic rhinoconjunctivitis (ARC) 3%. Of the 1008 (21%) allergy tested children 59% reported a positive test, but of the randomly selected children only 8% had a positive SPT. Children with AD were most frequently sensitized and children with ARC were most likely to have other allergy related disorders (70%). More boys than girls had an allergy related disorder or a positive allergy test. In conclusion, two in five had an allergy related disorder, but less than 10% had a positive SPT. Having one allergic disorder, especially ARC, increased substantially the risk of having another, and having AD was most strongly associated to a positive allergy test. Moreover, boys were more likely than girls to have an allergy related disorder or a positive SPT indicating a gender difference in the natural history of allergy related disorders.