MSCs induce thymic regeneration by repairing TECs. The proportion, number, and major histocompatibility complex class II (MHC II) levels of TECs, and Aire expression on mTECs were assessed in MSC-GVHD, non–MSC-GVHD, and non-GVHD recipients on day 20 and day 40 after HCT via flow cytometry. (A) Representative flow patterns of gated TECs shown as UEA-I (mTEC marker) vs Ly-51 (cortical TEC [cTEC] marker). (B) The proportion and number of mTECs and number of cTECs on day 20 and days 40 after HCT, data shown as the mean ± SE (n = 4-6). (C) Gated mTECs and cTECs shown as MHC II vs side scatter area (SSC-A). The percentage data of MHC II⁺ are shown as mean ± SE (n = 4-6). (D) Gated mTECs shown as Aire vs SSC-A. The percentage data of Aire-positive mTECs are shown as mean ± SE (n = 4-6). ∗∗P ＜ .01; ∗∗∗P ＜ .001; ∗∗∗∗P ＜ .0001.