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Early thymectomy during congenital heart disease repair may impair thymic output, but long-term effects across age groups remain incompletely defined. We evaluated T-cell receptor excision circles (TRECs) and a comprehensive panel of lymphocyte subsets in 20 adults (mean age, 29.6 years) and 16 children (mean age, 10.7 years) who underwent thymectomy within the first year of life, and in age- and sex-matched controls. TRECs were lower in patients than controls in adults (34 ± 25 vs. 79 ± 45 copies/μL; FDR-adjusted p = 0.001) and children (9 [7-15] vs. 95 [65-160] copies/μL; FDR-adjusted p < 0.0001). Total lymphocyte and T-cell counts were reduced in both age groups, mainly due to lower naïve CD4⁺ and CD8⁺ T cells, including recent thymic emigrants. Most non-naïve subsets did not differ significantly from controls. Regulatory T-cell (Treg) alterations differed by age: children showed broad reductions, whereas adults showed selective naïve Treg reduction. Early thymectomy is associated with persistent thymic output impairment, including in adults approximately three decades after surgery, and with age-specific Treg alterations.