Background: Recent studies have reported an increased risk of asthma in children after prenatal exposure to antibiotics, notably during third trimester due to altered vaginal bacterial flora. Associations could have been influenced by unmeasured confounders. Objectives: To assess the association between antibiotic use during pregnancy and the development of toddler asthma with a confounding minimizing crossover(casesibling) design. Secondary we wanted to assess the influence of time-invariant confounding by comparing results with a case-control design. Methods: We conducted this study using a linked mother-infant subset of the University Groningen prescription database IADB.nl. We conducted both a crossover study in which 1,228 children with asthma were compared to their own siblings without asthma, and a traditional matched case-control study. Maternal exposure was defined as at least 1 day of supply of systemic antibiotics during pregnancy. Children were considered to have asthma if they received at least 3 prescriptions for anti-asthma medication within a year before the fifth birthday. Conditional logistic regression was used to estimate crude and adjusted odds ratios (aOR). Sensitivity analyses were performed to estimate the potential influence of unobserved timevarying confounders. Results: The crossover analysis only showed an increase in the toddler's asthma risk if antibiotics were used in the third trimester of pregnancy (aOR 1.37 (95%CI 1.02-1.83)). The matched case-control study yielded a similar increase in the toddlers asthma risk after exposure in the third trimester (aOR 1.40(95%CI 1.15-1.47)). In addition, use of antibiotics, independent of trimester of pregnancy, was associated with an aOR of 1.46 (95%CI 1.33-1.58) in the matched case-control study. Conclusions: Prenatal exposure to antibiotics in the third trimester of pregnancy is associated with a small increased risk of childhood asthma. This association did not appear to be influenced by time-invariant confounders such as genetic predisposition. However the influence of time-variant confounders, such as disease severity, cannot be ruled out.