Cardioplegic reperfusion during a long term ischemic period interrupts cardiac surgery and also increase cellular edema due to repeated administration. We reviewed the clinical experiences on myocardial protection of one single perfusion with histidine-ketoglutarate-tryptophan (HTK) for infants. This retrospective study included 118 infants who underwent open-heart surgery between January 2004 and December 2007. We divided the entire cohort into two groups: In group H (n = 63), myocardial protection was carried out with one single perfusion with HTK solution, and in group S (n = 55) with conventional St. Thomas crystalloid cardioplegia. The duration of cardiopulmonary bypass (CPB) did not differ between these two groups, but the duration of aortic cross-clamping time in group H was significantly shorter than that in group S (p < 0.05). During reperfusion, the spontaneous re-beating rate was higher in group H (p < 0.05). There were no differences in doses of inotropic agent and creatinekinase (CK) values on postoperative day 1 between these two groups, but the level of CK in group H was significantly less than that in group S on postoperative day 2 (p < 0.01). The mortality in group H was lower than in group S (p < 0.05). The HTK group had shorter cross-clamping time and more frequent spontaneous defibrillation than St. Thomas group. We propose that HTK is valid for some complicated cardiac surgeries with long term cross-clamping time.