Background: Treatment with antibiotics in early childhood is effective for bacterial infections but may have long-term side effects. We evaluated the effect of broad-spectrum antibiotics treatment during the first two years of life in association with mode of delivery on subsequent onset of childhood type 1 diabetes. Methods: A Danish Nationwide cohort study included all singletons born during 1997-2010. Five national registers provided information on antibiotic redemption, outcome and confounders. The risk of type 1 diabetes with onset before the age of 15 years was assessed by Cox regression. A total of 858,201 singletons contributed 5,906,069 person- years, during which 1,503 children were diagnosed with type 1 diabetes. Results: Redemption of broad-spectrum antibiotics during the first two years of life was associated with an increased rate of type 1 diabetes during the following 13 years of life (HR 1.13; 95% CI 1.02 to 1.25), however, the rate was modified by mode of delivery. Broad- spectrum antibiotics were associated with an increased rate of type 1 diabetes in children delivered by either intrapartum cesarean section (HR 1.70; 95% CI 1.15 to 2.51) or prelabor cesarean section (HR 1.63; 95% CI 1.11 to 2.39), but not in vaginally delivered children. Number needed to harm was 433 and 562, respectively. The association with broad-spectrum antibiotics was not modified by parity, genetic predisposition or maternal redemption of antibiotics during pregnancy or lactation. Conclusions: Redemption of broad-spectrum antibiotics during infancy is associated with an increased risk of childhood type 1 diabetes in children delivered by cesarean section.