Background: Many countries have recorded the trends of food allergy (FA) prevalence. Little is known about epidemiological trends of childhood FA in China.Methods:In three cross-sectional surveys conducted in 1999, 2009, and 2019,the prevalence of and characteristic changes in FA in children aged ≤2 years were assessed and the outcomes were compared. All the children were recruited during well-baby check-ups at the Children's Hospital of Chongqing Medical University. All participants had a detailed medical history taken and underwent skin prick tests using ten commercial food extracts. Open food challenges were used for confirmation of FA.Results:The three studies included 1228 children (314 in 1999;401 in 2009; and 513 in 2019; response rate > 95 %).The prevalence of FA in 2009 (7.7%) and 2019 (11.1%) was significantly higher than that in 1999 (3.5%). However, there was no statistically significant difference in prevalence between 2009 and 2019 (P = 0.086). There was evidence of increased prevalence in CMPA between 1999 and 2019 (1.6% versus 5.7%;P=0.004);However, no statistic difference was found in egg allergy (2.9% versus 5.5%;P=0.21). The incidence of skin symptoms did not differ significantly over the study period, while the incidence of gastrointestinal symptoms increased significantly (18.2% in 1999, 12.9% in 2009, and 43.9% in 2019; P<0.05).Conclusions: The prevalence of FA in children rapidly increased after the 1990s and gradually stabilized after 2010. Cow’s milk has become the most common food allergen among children in Chongqing. The incidence of gastrointestinal symptoms as a manifestation of FA has increased significantly since 2010.