BACKGROUND : Taking oral antibiotics during childhood has been linked with an increased risk of childhood obesity. This study assessed any potential association in number of courses of antibiotics taken between 2-3 and 4-5 years of age and body mass trajectory up to age 5. METHODS : The study was a secondary analysis of 8186 children and their parents from the infant cohort of the Irish National Longitudinal Study of Children. Antibiotic use was measured by parental recall between ages 2-3 and 4-5. Longitudinal models described the relationship between antibiotic exposure and body mass index (BMI) standard deviation scores and binary outcomes, and examined interactions between covariates, which included socioeconomic status, diet assessed by food frequency questionnaires and maternal BMI. RESULTS : Any antibiotic usage between 2 and 3 years did not predict risk of overweight or obesity at age 5. Four or more courses of antibiotics between 2 and 3 years were independently associated with obesity at age 5 (odds ratio 1.6, 95% confidence interval 1.11-2.31). Effect size was modest (coefficient + 0.09 body mass SD units, standard error 0.04, P = 0.037). Maternal BMI modified the relationship: ≥ 4 courses of antibiotics between 2 and 3 years were associated with a + 0.12 body mass SD units increase in weight at age 5 among children of normal-weight mothers (P = 0.035), but not in children of overweight mothers. CONCLUSIONS : Number of antibiotic courses, rather than antibiotic use, may be an important factor in any link between early antibiotic exposure and subsequent childhood obesity. Research is needed to confirm differential effects on babies of normal versus overweight/obese mothers independent of socioeconomic factors.