Abstract Radiotherapy and/or chemotherapy in cancer treatment causes lymphopenia, which favors autoimmunity. Also, coinhibitory receptor blockade triggers immune-related adverse events in more patients than it cures of cancer. Having shown that PD-1 coinhibitory receptor is required in newly generated T cells (NGTC) to prevent lymphopenia-induced autoimmunity, our objective was to determine if the coinhibitory receptor BTLA is also required to establish tolerance in NGTC during lymphopenia. NGTC from thymocytes or established T cells from splenocytes of wildtype (WT) or BTLA−/− B6 mice were adoptively transferred to lymphopenic Rag−/− B6 mice. Sorted WT or BTLA−/− CD8 or CD4 single-positive (SP) thymocytes were adoptively transferred to Rag−/− mice not expressing MHC II (CiiTA−/−) or lacking MHC I (KbDb−/−), respectively. Disease was assessed by macroscopic appearance and weight loss. About 65% (5/8) recipients of BTLA−/− NGTC developed overt autoimmunity, while 4/4 recipients of BTLA−/− splenocytes were disease-free. 10/10 recipients of BTLA−/− CD8 SP T cells showed progressive weight gain. In contrast, 11/11 BTLA−/− CD4 SP T cell recipients had diarrhea, piloerection, hunched appearance, and progressive weight loss from 3–8 weeks post thymocyte transfer (p<0.0001). 3/11 BTLA−/− CD4 SP T cell recipients developed dermatitis post thymocyte transfer. Overt autoimmunity was evident in all WT Rag−/− (n=11) and Rag−/− KbDb−/− (n=4) recipients of thymocytes, but not in any of the CiiTA−/− recipients (n=4). There were no signs of disease in the recipients of WT NGTC. Our study suggests that BTLA is required to establish tolerance in NGTC. Disease in BTLA−/− thymocyte recipients was mediated by the CD4+ T cells and was dependent on MHC II.