The DIABIMMUNE three-country cohort dataset tracks infants from Finland, Estonia, and Russia with similar HLA genetic risk for type 1 diabetes, collecting comprehensive longitudinal data including monthly stool microbiome sequencing (16S rRNA and whole-genome shotgun), clinical records, and lifestyle factors. It investigates the role of gut microbiome variations and early immune education in allergy and autoimmune disease development, providing valuable data to explore microbial and genetic influences on immune-related conditions