The aim of this prospective cohort study was to reveal the effect of mode of delivery, independently of other confounders, on the risk of overweight or obesity in infants (age-sex-specific body mass index >= 85th percentile). In total, 294 infants born in the Rize Province between November 1 2013, and September 30 2014, and their mothers were included; all infants attended well-child visits with the same family physician for up to two years. Multivariate logistic regression analysis was performed to determine significant associations. The odds ratio (OR) of overweight and obese children aged 2 years in association with the mode of delivery was estimated by logistic regression analysis. In crude analysis, compared with vaginal delivery, the use of Caesarean Section delivery was associated with the risk of childhood overweight or obesity [OR: 2.06; 95% confidence interval (CI): 1.08-4.30]. Even after multivariate adjustment, this increased risk persisted (adjusted OR: 1.93; 95% CI: 1.13-4.18). In conclusion, significantly increased risk of overweight or obesity was found in 2-year-old children born via Caesarean delivery.Impact statement What is already known on this subject?Although there are studies on the relationship between childhood obesity and Caesarean Section delivery, results are inconsistent. What do the results of this study add?This is the first prospective cohort study showing the effect of Caesarean delivery on childhood obesity in Turkish children. What are the implications of these findings from clinical practice and/or further research?Future studies should further investigate the exact reasons underlying the association between Caesarean delivery and childhood metabolic syndrome.