Aims To investigate the effect of Caesarean section on gastrointestinal symptoms, atopic dermatitis and sensitization to nutritional allergens in infants.Methods A total of 865 healthy full‐term neonates with parental history of allergy participating in the prospective German Infant Nutritional Intervention Program (GINI) were exclusively breastfed during the first four months of life and had a one year follow‐up. Data were obtained by follow‐up visits at age 1, 4, 8, and 12 months, weekly diaries for the first six months, and measurement of total and specific IgE at birth and 12 months.Results Infants born by Caesarean section (147/865, 17%) had a greater risk of diarrhoea (ORadj 1.46, 95% CI 1.022–2.10) and sensitization to food allergens, both in adjusted (ORadj 2.06, 95% CI 1.123–3.80) and stratified analyses (by cord blood IgE). Caesarean delivery was not associated with colicky pain and atopic dermatitis.Conclusion Caesarean delivery might be a risk factor for diarrhoea and sensitization in infants with family history of allergy. Further research in this area seems warranted as choosing Caesarean section becomes increasingly popular.