Objective To ascertain the significance of food intolerance-specific IgG antibody detection and suspicious risk factors of food intolerance in neonates. Methods The food intolerance-specific IgG antibodies in serum were measured by Enzyme-Linked Immunosorbnent Assay (ELISA) in 60 neonates who were considered to be food intolerance(especially cow's milk) and in 60 control neonates,analyzed the influential factors of IgG results by Logistic regression models. Results 93.3% of patients appeared positive results in different food IgG antibodies;In the single factor analysis,3 indexes were obviously significant (P<0.05) and 2 of them were also significant in the multi-factor stepwise regression analysis (P<0.05);There were no relationships between the sex,delivery ways,gestational age,smoking during pregnancy and the result of IgG results. Conclusions Neonates can show a series of food intolerance symptoms in the neonatal period and specific IgG antibody detection has higher positive rate.The results indicate that family history of atopic diseases was the risk factor of specific IgG positive result,while breast feeding was protective.Raising awareness for food intolerance of neonates,and intervention should be given to avoid a serious effect on growth as early as possible.