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Antibiotic use during infancy alters gut microbiota and immune development, and is associated with an increased risk of several childhood diseases. The impact of prenatal antibiotic exposure is unclear.To determine and characterise the association of prenatal antibiotic exposure and childhood IBD, diabe-tes, allergy, cholestasis and connective tissue disorders.Population-based cohort study using admin-istrative healthcare data. Antibiotic use was determined from prescription records. Diseases were defined using hospitalisation records, physician billing claims, and pre-scription records. Associations were determined using Cox regression and expressed as hazard ratios (HR) and 95% confidence intervals (CI).General population in Manitoba, Canada.2 13 661 mother-child dyads born from 1996–2012.Maternal antibiotic use.childhood IBD, diabetes, allergy, cholestasis and connective tissue disordersIn our study population, 36.8% of infants were prenatally exposed to antibiotics. Prenatal antibiotic ex-posure was associated with an increased risk of IBD (HR 1.59 (1.46–1.71), cholestasis (1.46 (1.21–1.77)) and severe allergies (1.08 (1.01–1.15)) when controlling for maternal disease (same as child), sex, location of residence, gestational age, number of siblings, and postnatal antibiotic exposure during infancy. Higher numbers of prescriptions increased the risk for most outcomes. However, maternal antibiotics use during the 9 months before pregnancy and 9 months postpartum were similarly associated with several of the outcomes.Maternal antibiotic use before, during and after pregnancy was associated with a modest, dose-dependent increase in IBD, cholestasis, and allergy risk among offspring. While our study does not support a pregnancy-specific causal relationship be-tween maternal antibiotic use and these diseases, it does provide additional warning to prescribe and use antibiot-ics judiciously, both in pregnancy and infancy.