The diagnostic accuracy of the skin prick test (SPT) in food allergy is controversial. We have developed diagnostic cut-off levels for SPT in children with allergy to cow milk, egg and peanut. Based on 555 open food challenges in 467 children (median age 3.0 yr) we defined food-specific SPT weal diameters that were ‘100% diagnostic’ for allergy to cow milk (≥8 mm), egg (≥7 mm) and peanut (≥8 mm). In children <2 yr of age, the corresponding weal diameters were ≥6 mm, ≥5 mm and ≥4 mm, respectively. These SPT cut-off levels were prospectively validated in 90 consecutive children ≤2 yr with challenge-proven food allergy. In young infants under 6 months of age who have not previously been exposed to a particular food item, the SPT were often negative or below the diagnostic cut-off but reached the diagnostic cut-off at the time of challenge in the second year of life. We assessed the diagnostic agreement between food-specific immunoglobulin E (IgE) antibody levels and SPT in a cohort of 820 infants and children under 2 yr of age (median age 13.1 months) with suspected allergy to cow milk, egg or peanut. When applying published 95%-positive predictive CAP values, the diagnostic accuracy of SPT and IgE antibody levels was similar for cow milk, but SPT was more sensitive in diagnosing allergy to egg (p < 0.0001) and peanut (p < 0.0001). Further studies are required to define age-specific diagnostic IgE antibody and SPT cut-off levels use in infants under 2 yr of age with suspected food allergies.