Background: Previous studies, mainly questionnaires have reported associations between some indoor environmental factors and allergic diseases. Our aim was to investigate the possible association between objectively assessed indoor environmental factors and clinically confirmed asthma, rhinoconjunctivitis and atopic dermatitis. Method: A crosssectional case-cohort study (n = 500) based on 2835 children, aged 3–5 years, responding to a questionnaire, consisted of 300 subjects randomly selected and 200 cases with at least two parentally reported doctor diagnosed allergic diseases (asthma, allergic rhinoconjunctivitis or atopic dermatitis). The same physician conducted a clinical examination of all the 500 children including structured interview on allergic heredity, clinical and medical history. Specific s-IgE against inhalant and food allergens was determined. The homes were investigated by inspectors assessing air change rates, relative humidity, temperature, CO2, and dust samples were collected for analyses of indoor allergens, phthalates, nicotine and polyaromatic hydrocarbons. The diagnosis of allergic disease was based on internationally accepted criteria. Result: In the base group (n = 300) asthma was clinically diagnosed in 5.1%, rhinoconjunctivitis in 5.1% and atopic dermatitis in 11.0%. Air change rates were below the recommended 0.5 in 56% of all the homes. Air change rates were higher among children asthma/rhinoconjunctivitis (P