The skin prick test is the most widely used test for detecting IgE-mediated food hypersensitivity. Our study aimed to define firstly the correlations between results obtained with prick tests using commercial extracts and fresh foods, and secondly the correlations between these results and those obtained with labial and/or oral challenge. We compared the wheal diameters read at 15 min with commercial extracts and fresh foods, for four foods, in 430 children with suspected food allergy. For cow's milk, wheal diameters were larger with commercial extracts, but the difference was not significant. Conversely, wheal diameters were significantly larger with fresh foods for the other food allergens. Skin prick tests were positive in 40% of cases with commercial extracts and in 81.3% with fresh foods. The overall concordance between a positive prick test and positive challenge was 58.8% with commercial extracts and 91.7% with fresh foods. These results indicate that fresh foods may be more effective for detecting the sensitivity to food allergens. Fresh foods should be used for primary testing for egg, peanut, and cow's milk sensitivity.