Prevention of allergic diseases depends on early identification of clinical markers preceding such disorders. This study describes the natural course of sensitization as measured by skin prick test (SPT) and specific immunoglobulin E (S-IgE) and analyses the association between early sensitization patterns and subsequent allergic disease at 6 yr of age. In an ongoing population-based birth cohort study of 562 children, follow-up visits were performed at 0, 3, 6, 9, 12, 18, 36, and 72 months. Visits included an interview, physical examination, SPTs, and S-IgE measurements for 12 food and inhalant allergens. The frequency of S-IgE sensitization to ≥1 inhalant allergen was constant from 0 to 6 months (9–10%), decreased at 12–18 months before increasing from 36 months onwards. S-IgE sensitization to at least one food allergen remained constant from 0 to 6 yr. SPT sensitization to food and inhalant allergens appeared from 3 and 12 months, respectively. Early food sensitization (S-IgE) between 3 and 18 months was found to be significantly (p < 0.05) associated with atopic dermatitis (OR: 4.0 [1.6–9.9]) and asthma (OR 4.0 [1.1–12.5]) at the age of 6 yr. Children with atopic dermatitis, asthma, or rhinoconjunctivitis, and sensitization at 6 yr, were sensitized to food allergens to a large extent (53%, 42%, and 47%, respectively) already at 6 months. Early inhalant sensitization (S-IgE) did not increase the risk of later allergic disease. Early atopic dermatitis (0–18 months) was also highly associated with subsequent allergic disease. Children with early food sensitization and/or atopic dermatitis would be a proper target group for future interventional studies.