There is a paucity of information on food hypersensitivity (FHS) in young children and there are even fewer population-based studies in this area. The aim of the study was to determine the prevalence of parentally reported FHS, and objectively diagnosed FHS amongst six-year-old children and to establish the rates of sensitization to key allergens. This population-based cohort study recruited 798 6-year-olds resident on the Isle of Wight (UK). Sensitization rates, reported rates of FHS and objectively assessed FHS was established using food challenges. A total of 94 (11.8%) 6 yr olds reported a problem with a food or food ingredient. The rate of sensitization to the pre-defined panel of food allergens was 25/700 (3.6%). Based on open food challenge and/or suggestive history and skin tests, the prevalence of FHS was 2.5% (95% CI 1.5–3.8). Based on double-blind challenges, a clinical diagnosis or suggestive history and positive skin tests, the prevalence was 1.6% (95% CI 0.9–2.7). The rates of perception of FHS are higher than the prevalence of sensitization to main food allergens and the prevalence of FHS based on food challenges. Milk, peanut and wheat were the key food allergens amongst those with positive challenges.