The active metabolite of vitamin D, 1,25-(OH)2D3, has immunomodulatory properties in addition to its more established action on bone and calcium metabolism. Recently vitamin D has been proposed as one of several environmental factors responsible for the increase in atopic diseases during the last decades. The objective of this study was to determine whether the estimated dose of dietary vitamin D3 during the first year of life is associated with atopic diseases up to the age of 6 years. In a prospective birth cohort study 123 six-year-old children were investigated for the cumulative incidence of atopic dermatitis, allergic rhinitis or asthma by means of a postal questionnaire. Their vitamin D3 intake during infancy was recorded in a previous study and the relationship between lower or higher vitamin D3 intake and atopic illness later in childhood was assessed. Atopic manifestations were more prevalent in the group with higher intake of vitamin D3. Although small, this study supports previous investigations suggesting a role of vitamin D intake during infancy in the development of atopic allergy later in childhood. If these findings are confirmed in prospective controlled clinical trials, prevention through modified vitamin D3 supplementation in infancy could be discussed to reduce the burden of atopic illnesses.