Objective: To preliminarily explore the association of pregnancy factors with cow's milk protein allergy in infants. Methods: This study was based on data from a subcohort of a study called genetic susceptibility to cow's milk allergy in Chinese children, including infants born in Peking University People's Hospital between March 1, 2020, and December 31, 2020. The infants were divided into a cow's milk protein allergy (CMPA) group and a control group according to whether they had developed cow's milk protein allergy at the age of 1 year. We retrospectively collected the clinical data of infants and their mothers before and during pregnancy, and analyzed the association of multiple factors during pregnancy with cow's milk protein allergy in infants. Results: A total of 278 infants were enrolled in this study, including 52 infants with CMPA and 226 infants without CMPA. Among them, there were 143 boys and 135 girls. The proportion of male infants in the CMPA group (69.2%) was higher than that in the control group (47.3%), and the difference was statistically significant (P=0.004). There were no significant differences in the distribution of birth weight, gestational age at birth, low-birth-weight infants, premature, umbilical cord entangle neck, and neonatal asphyxia between the CMPA group and the control group (P>0.05). The proportion of mothers complicated with autoimmune diseases, anemia or antibiotics exposure during pregnancy in the CMPA group was higher than that in the control group, and there were statistical differences between the two groups (P < 0.05). There was no significant difference in the distribution of other pregnancy complications between the two groups (P>0.05), such as eclampsia/preeclampsia, chronic hypertension/gestational hypertension, diabetes/gestational diabetes, thyroid diseases, and so on. There was no significant difference in the overall distribution of some blood routine indexes during pregnancy between the CMPA group and the control group (P>0.05). Multivariate Logistic regression analysis showed that male infant, mothers complicated with autoimmune diseases or anemia, antibiotic exposure during pregnancy were independent risk factors for cow's milk protein allergy. Conclusion: Male infant, mothers complicated with autoimmune diseases or anemia, antibiotic exposure during pregnancy were independent risk factors for cow's milk protein allergy.