The aim of this review is to review the literature concerning the role of several PTPs—PTPN22, PTPN2, PTPN6, PTPN11, PTPσ, DUSP2, DUSP6 and PTPRK—at the level of the intestinal mucosa in inflammatory bowel disease (IBD), celiac disease (CeD) and type 1 diabetes (T1D) in both in vitro and in vivo models. Here, PTPN11 is linked to cranioectodermal dysplasia.