BACKGROUND: Defects of thymic stromal cell development may lead to congenital athymia and severe immunodeficiency. Allogeneic thymus transplantation is the only recognized effective therapy to reconstitute naive T cells in these rare cases, increasingly diagnosed because of worldwide newborn screening. Nevertheless, data on long-term outcomes are still missing. OBJECTIVE: We sought to report the clinical and immunologic outcomes of an adult with R255X homozygous FOXN1 mutation, followed for 19 years after thymus transplantation with effective immune reconstitution attested by clearance of BCG dissemination and reconstitution of the naive T-cell compartment with a fully diverse repertoire. METHODS: Longitudinal autoimmunity screening and immune profiling were complemented with T-cell studies by high-dimensional spectral flow cytometry (age 18 and 20 years) and single-cell RNA sequencing (age 18 years) combined with T-cell receptor and cell surface protein sequencing alongside age-matched controls. RESULTS: The uneventful clinical report contrasted with the progressive decline in circulating T-cell counts (<
400 cells/μL), with marked contraction of the naive compartment and lack of terminal differentiation. CD4 T cells featured a unique transcriptional signature supporting a distinct biology of T cells developed in an allogeneic thymus implant. Regulatory T cells presented a suppressive signature, which may explain the absence of autoimmune manifestations. The expanded oligoclonal population of double-negative αβ T cells identified before transplant persisted with similar phenotype with transcriptional evidence of a role for the epidermal growth factor receptor pathway in its maintenance. CONCLUSIONS: This rare case supports a distinct biology of T cells educated in allogeneic thymus, with poor naive T-cell sustainability emphasizing the need for research on immune reconstitution mechanisms.