This study aims to examine the relationship between infant-feeding practices and American Indian infants' gut microbiome--laying the foundation of a research program aimed at identifying potential aetiologies of childhood obesity in this population. Previous studies have emphasised the high prevalence of obesity in American Indian infants, but its underlying causes remain unclear. We received funding from the University of Washington to examine attitudes towards breastfeeding and formula feeding in American Indian mothers, their dietary and physical activity habits and the yield, quality and diversity of their infants' gut microbiome. Our study combines the strengths of qualitative and quantitative data with DNA sequencing. Results will be used to propose a larger study aimed at clarifying aetiologies of childhood obesity in this population and to identify prevention strategies. This protocol describes the theoretical basis of the study, rationale for the target population, study design, participant recruitment and data analysis plan.