MAIT cells develop in the thymus where they are selected by double-positive thymocytes presenting microbial metabolites on MR1 and, thereby, acquire Plzf and memory-effector phenotypes. In parallel, interactions with MR1-presenting epithelial cells can select “MAIT” cells which resemble conventional T cells. Notwithstanding, MAIT cells with different maturity and effector phenotypes can be found in the periphery and vary according to the organ. Here, the stages of MAIT development were defined as: MAIT0 (CD24+), MAIT immature1 (MAITi1, CD24-Plzf-), MAITi2 (Plzf+Tbet-Rorgt-), MAIT1 (Plzf+Tbet+) and MAIT17 (Plzf+Rorgt+). We used several approaches, including bone-marrow chimeras, thymus transplants and various cre-mouse lines, to selectively restrict or delete MR1 expression and analyzed their impact on MAIT development and peripheral homeostasis. Additionally, we investigated MAIT cell egress from the thymus and tissue colonization. Exit of MAIT cells from the thymus relied on S1PR receptors. Indeed, after treatment with S1PR-antagonist FTY720, not only MAIT1 and MAIT17 accumulated in the thymus but also MAITi1 and MAITi2. Adoptive transfer of these subsets into immune-replete hosts demonstrated tissue tropism of MAIT1 to the liver and MAIT17 to the lung while MAITi1 colonized preferentially the lymph nodes(LNs). With time, the number of transferred MAIT17 increased in the LNs but not the organs, suggesting that these cells first colonize the tissues and subsequently the LNs. As both skin and intestine were refractory to colonization in immune-replete hosts, we repeated these experiments with immune-compromised recipients. While MAIT17 colonized preferentially the skin, MAITi2 went preferentially to the gut and mesenteric-LN where they further differentiated into MAIT17 and MAIT1/17(Tbet+Rorgt+). Expansion and maintenance of these populations depended on MR1. Finally, thymic MAITi2 re-expressed Ccr9 and appear to rely on it to colonize the gut. Altogether, we propose a two-step selection process for thymic MAIT cells which acquire subset-specific tissue-tropism in the thymus and differentially colonize peripheral organs.