Skin Prick Test (SPT's) are performed to identify the causes of allergy. However, low diagnostic accuracy is a limitation to SPT, for which many possible causes have been suggested. The protein composition and allergenicity of crude allergen extracts from foods and commercial allergen extracts for SPT were analyzed. Clinical significances of SPT using crude allergen extracts from foods were compared with those using commercial allergen extracts. A total of 292 atopic dermatitis patients were involved in this study. Crude allergen extracts were prepared from milk, egg white, egg yolk, and soybean. The protein composition of food allergen extracts and commercial allergen extracts of milk, whole egg, white, egg yolk, and soybean were compared by SDS-PAGE. The allergenicity was tested by the immunoblotting method using immune sera. SPTs were performed using crude and commercial allergen. Double-blind placebo- controlled food challenge (DBPCFC) was performed to verify the SPT results and to compare the clinical significance of crude and commercial allergen extracts. Protein composition differed markedly between crude and commercial allergen extracts. By immunoblotting, crude and commercial allergen extracts showed different allergenicity. The SPT results using crude and commercial allergen extracts showed significant differences. The prevalence of milk, egg and soybean allergy was over 35% in atopic dermatitis. The accuracy of SPT using crude allergen extracts from foods was significantly higher than that using commercial allergen extracts. In the case of soybeans, the result of SPT using commercial allergen extract was clinically insignificant for the prediction of soybean allergy. The source of allergen extract was very important for the appropriate SPT in food allergy. The accuracy of SPT might be improved using the appropriate allergen source for food allergy.