The present study was conducted to evaluate the effect of thymectomy during open heart surgery on immunological function of T lymphocytes in the treatment of children with congenital heart disease (CHD). No significant difference was found in the sjTREC level between pre-thymectomy and post- thymectomy in the non-thymectomy group and the small partial resection group (P>0.05) However, the sjTREC level decreased from the pre-surgical level at 1 month (P<0.01) and 12 months (P<0.01) in the sub-total resection group. No differences were found in proportions of CD3, CD4 and CD8 lymphocytes, proliferative ability of lymphocytes and expression of IL-2, IL-4 and IFN-γ after surgery between controls and three groups of patients (P>0.05). In the sub-total resection group, respiratory infection frequency (4.7±1.7 times) did not differ significantly from control group one year after surgery (P>0.05); however, mean days of anti-infection were significantly increased (P less than 0.01). In conclusion, sub-total thymectomy leads to a decrease in the sjTREC level in CHD children, whereas the function of peripheral mature T lymphocytes is normal.