Crohn’s disease (CD) is chronic complex autoimmune condition characterized by inflammation of the gastrointestinal tract. Pediatric CD diagnosed in patients younger than 20 years of age comprises 30% of all diagnosed CD. There is significant data to suggest that CD may represent an inappropriate T-cell mediated immune response towards self-antigens and commensal microbiota in a genetically susceptible host. To understand the T cell-mediated pathogenesis in pediatric CD we performed scRNA-seq analysis and concurrent flow cytometric analysis on mucosal biopsies from the multiple locations along the gastrointestinal tract and paired peripheral blood lymphocytes in pediatric CD and compared these to matched samples from patients with pediatric Functional Gastrointestinal Disorders (FGID).