The gut microbiome is suggested to play a role in the pathogenesis of autoimmune disorders such as type 1 diabetes. Evidence of anti-islet cell autoimmunity in type 1 diabetes appears in the first years of life, however little is known regarding establishment of the gut microbiome in early infancy. Here, we sought to determine whether differences were present in early composition of the gut microbiome in children who developed anti-islet cell autoimmunity. We investigated the microbiome of 298 stool samples prospectively taken up to age 3 years from 22 case children who developed anti-islet cell autoantibodies, and 22 matched control children who remained islet autoantibody negative in follow-up. The microbiome changed markedly during the first year of life, and was further affected by breast-feeding, food introduction, and birth delivery mode. No differences between anti-islet cell autoantibody positive and negative children were found in bacterial diversity, microbial composition, or single genus abundances. However, substantial alterations in microbial interaction networks were observed at age 0.5 and 2 years in the children who developed anti-islet cell autoantibodies. The findings underscore a role of the microbiome in the pathogenesis of anti-islet cell autoimmunity and type 1 diabetes.