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Continuous locked suture technique in arterial anastomosis was used in a rat heterotopic small bowel transplantation model. Blood loss, time consumption and success rate of the technique, as well as long-term blood flow and histological changes of arterial anastomosis and intestinal graft were compared with the traditional simple continuous suture technique. The results showed that the time consumption was similar between the two techniques while the continuous locked suture technique had a higher success rate (P = 0.016) and was more secure than the simple continuous suture technique. Moreover, it provided a higher long-term blood flow. Under light microscopy and electron scanning microscopy, the anastomosis of continuous locked suture technique showed significantly less stenosis than those of simple continuous suture technique. No difference was found between the two techniques considering the graft intestinal histological changes. In conclusion, the continuous locked suture technique was a more superior technique than simple continuous suture technique in arterial end-to-side anastomosis considering long-term hemodynamics.