Background: This study aimed to investigate the associations of pre-pregnancy body mass index (BMI) and gestational weight gain (GWG) with anogenital distance (AGD) among newborns. Methods: The study included 556 mother-newborn pairs from the Jiashan birth cohort. AGD was measured as AGDAP (from the center of the anus to the anterior base of the penis, where the penile tissue meets the pubic bone) and AGDAS (from the center of the anus to the posterior base of the scrotum, where the skin changes from rugate to smooth) in males and AGDAC (from the center of the anus to the clitoris) and AGDAF (from the center of the anus to the posterior convergence of the fourchette) in females. Multiple linear regression models were used to estimate the associations of pre-pregnancy BMI and GWG, with AGD. Results: After adjusting for pre-pregnancy BMI and other potential confounders, male newborns whose mothers had excessive GWG had shorter AGDAP than those whose mothers had normal GWG. Male newborns whose mothers had normal pre-pregnancy BMI and inadequate/excessive GWG had shorter AGDAP than the reference group where mothers had normal pre-pregnancy BMI and GWG in stratified analyses. Conclusion: Gestational weight gain during pregnancy was associated with AGD in newborns in this birth cohort. Plain language summary: In China, the prevalence of underweight and overweight/obesity remained high among women. Appropriate pre-pregnancy body mass index (BMI) and gestation weight gain (GWG) were critical to reduce the risk of adverse birth outcomes. The anogenital distance (AGD) was measured as an indicator of neonatal reproductive function and was associated with adverse reproductive outcomes in adults. Thus, we investigated the associations of both sub-optimal pre-pregnancy BMI, as well as GWG, with AGD among newborns to draw a picture about their effect on offspring reproductive health. A total of 556 mother-newborns were included in the study from the Jiashan birth cohort in China. We extracted information about maternal lifestyles, social demographic characteristics, diet, and medical history from questionnaires conducted during 8–16 gestational weeks and medical records. AGD among newborns was measured within 3 days of delivery. We found that maternal excessive GWG was associated with shorter AGD in male newborns after adjusting for maternal pre-pregnancy BMI in multiple linear regression models. The study also suggested that maternal inadequate GWG was associated with a shorter AGD in male newborns, which needed to be corroborated in further studies with a larger sample size. In conclusion, health professionals shall implement sufficient intervention to prevent suboptimal GWG during prenatal checkups. [ABSTRACT FROM AUTHOR]