CD1d-restricted natural killer T cells and MR1-restricted mucosal associated invariant T (MAIT) cells constitute two subsets of unconventional T cells that are phylogenetically conserved. Therefore, they are thought to play an essential role within the immune system. MR1-restricted MAIT cell selection is dependent upon B cells, and their accumulation in the gut lamina propria and mesenteric lymph node requires the commensal bacterial flora. These features suggest that MAIT cells could be involved in tolerance or immunity to infections in the gut. As for natural killer T cells, the recent identification of one endogenous ligand, isoglobotrihexosylceramide, and of a family of bacterial agonists is an important advance for understanding their thymic selection and their role during infections.