Introduction: The first 1000 days of life could contribute to individual susceptibility to the later development of chronic non-communicable diseases. Nutrition in early life appears to be an important determinant factor for a sustainable child's health. In this study, we propose to investigate the impact of exclusive breast feeding on gut health in children. Methods and analysis: A prospective cohort of newborns (n=350) will be recruited at birth and followed up to 4 years of age. The main objective is to evaluate the link between exclusive breast feeding for at least 3 months and the gut health of the child at 4 years. The primary endpoint of assessment of gut health will be based on the non-invasive measurement of faecal secretory IgA (sIgA) as a sensitive biomarker of the intestinal ecosystem. The presence of gastrointestinal disorders will be defined according to the clinical criteria of Rome IV. Information on parent's nutritional habits and life style, breastfeeding duration and child's complementary feeding will be collected along the follow-up. Cord blood cells and plasma at birth will be purified for further analysis. The meconium and stools collected at birth, 6 months, 2 years and 4 years of age will allow sIgA analysis. Ethics and dissemination: This clinical study has obtained the approval from the national ethical committee. We plan to publish the results of the study in peer-review journals and by means of national and international conference. Trial registration number: NCT04195425.