Background Fetal programming during in utero life defines the set point of physiological and metabolic responses that lead into adulthood; events happening in “the first 1,000 days” play a role in the development of non-communicable diseases (NCDs). The infant gut microbiome is a highly dynamic organ, which is sensitive to maternal factors and environmental insults; it modifies its composition over the host’s lifespan and is one of the elements driving this intergenerational NCDs' transmission. The A.MA.MI (Alimentazione MAmma e bambino nei primi MIlle giorni) project aims at investigating the possible correlation between pre-natal and post-natal factors and the infant gut microbiome composition, during the first year of life at different follow-up. We describe the study design of the A.MA.MI Study and present some preliminary results.Methods A.MA.MI is a longitudinal, prospective, observational study that includes a group of mother-infant pairs (n=63) attending the Neonatal Unit, Fondazione IRCCS Policlinico San Matteo, Pavia (Italy). The study was planned to provide data collected before discharge (T0) and at 1,6,12 months after birth (T1,T2,T3). Maternal and infant anthropometric measurements are assessed at each time. Other variables evaluated are pre-pregnancy/gestational weight status (T0), maternal dietary habits/physical activity (T1-T3); infant medical history, type of feeding, antibiotics/probiotics/supplements use, environment exposures (e.g cigarette smoking, pets, environmental temperature) (T1-T3). A child stool sample was planned to be collected at each time and analyzed using metagenomics 16S ribosomal RNA gene sequence-based methods. Maternal urine samples were planned to be collected at T3 to investigate pollutants exposure (Phthalates, Bisphenol A and Hydroxypyrene).Results Concerning the birth mode (cesarean section vs. vaginal delivery) significant differences were found only at genera and species levels (T0). A significantly higher relative abundance of Firmicutes was found in meconium of infants born from mothers affected by overweight/obesity, when compared to women with normal weight before pregnancy (T0). Regards type of feeding (breastfed vs formula-fed) the gut microbiota composition differed significantly only at genus and species level (T1).Conclusion These preliminary and explorative results confirmed that pre-pregnancy BMI, mode of delivery and infant factors could affect the infant microbiota composition at different levels.