T cells play an important role in the immune system by detecting microbial molecules that signal infection. While most studies have focussed on T cells that detect foreign peptides, recent studies have shown that a major T cell population called MAIT cells recognise microbial vitamin B2 derivatives presented by the molecule, MR1. Using MR1 tetramers, we describe how MAIT cells develop in the thymus and identify key checkpoints that control the maturation of these cells.