The mammalian intestine harbors abundant T cells with high motility, where these cells can affect both intestinal and extraintestinal disorders. Growing evidence shows that gut-derived T cells migrate to extraintestinal organs, contributing to the pathogenesis of certain autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). However, three key questions require further elucidation. First, how do intestinal T cells egress from the intestine? Second, how do gut-derived T cells enter organs outside the gut? Third, what is the pathogenicity of gut-derived T cells and their correlation with the gut microenvironment? In this Opinion, we propose answers to these questions. Understanding the migration and functional regulation of gut-derived T cells might inform precise targeting for achieving safe and effective approaches to treat certain extraintestinal autoimmune diseases.