There is insufficient evidence to confirm the association between breastfeeding and allergic outcomes later in life. This study aimed to determine the relationships between different breastfeeding patterns and allergen sensitizations and risk of developing atopic diseases in early childhood. A total of 186 children from a birth cohort in the Prediction of Allergies in Taiwanese Children study for a 4-year follow-up period were enrolled. Total serum immunoglobulin E (IgE) levels and specific IgE antibodies against food and inhalant allergens were measured sequentially at 6 months as well as at 1, 1.5, 2, 3, and 4 years of age. A significantly lower prevalence of milk sensitization was found in children at ages 1 and 1.5 years who were exclusively or partially breastfed for ≥6 months. Breastfeeding ≥6 months was significantly associated with a reduced risk of developing eczema but not allergic rhinitis and asthma at ages 1 and 2 years. Compared with exclusive breastfeeding ≥6 months, partial breastfeeding <6 months was significantly associated with an increased risk of developing eczema at ages 1 and 2 years. As with exclusive breastfeeding, partial breastfeeding for at least 6 months appears to be associated with a reduced prevalence of milk sensitization as well as a reduced risk of developing eczema in early childhood.