Purpose of review There has been increasing interest in the contents and function of the microbiota, as it relates to pediatric inflammatory diseases. Here, we discuss the factors underlying the development of the microbiota, its role in juvenile idiopathic arthritis (JIA) and prospects for therapeutic interventions in the microbiota. Recent findings The human microbiota undergoes a succession of changes, until it reaches a mature form. A variety of early-life exposures, including mode of delivery and form of feeding, can affect the contents of the microbiota and possibly impact upon long-term risk of developing autoimmune diseases. The microbiota is altered in children with JIA, including elevated Bacteroides genus in JIA as a whole and decreased Faecalibacterium prausnitzii in pediatric spondyloarthritis. Although there are limited data so far indicating that microbiota-based therapies can result in therapeutic improvement of arthritis, most of the data are on adults and thus may not be applicable to children. Summary Perturbations of the microbiota during childhood may result in the development of a microbiota associated with increased risk of pediatric rheumatic illness. Whether the microbiota can be targeted is a focus of ongoing research.