The human thymus is required for establishment of a T-cell pool in fetal life, but postnatal thymectomy is not known to cause immunodeficiency. T-cell emigration from thymus (thymic recent emigrants [TRECs]) is a continuous thymic-dependent process. We studied TREC levels pre-and post-partial thymectomy in children undergoing cardiac surgery. TRECs were quantitated by real-time PCR in peripheral blood lymphocytes of 24 children (0 to 12 years). TREC values were 47916 ؎ 9271 pre-partial thymectomy and 33157 ؎ 8479 postpartial thymectomy in 11 paired patients (P ‫؍‬ 0.014). Interval between pre-and post-partial thymectomy was 8.8 days ؎ 5.8 days. Another group of 8 children had 30384 ؎ 9748 TRECs 16 days to 6 years post-partial thymectomy. There was a significant drop in TREC values post-partial thymectomy in the immediate postoperative period compared to prethymectomy TREC levels. While decreased thymic output may persist, the long-term implications were not evaluated in this patient population.