Background: Regarding the limited number of studies on the feasibility of resection and repair of the small intestine by ligasure, we performed this study to compare ligasure with linear stapler for the previously mentioned operation.Methods: This phase 1 clinical trial study was performed in Ghaem Hospital, an educational hospital affiliated to Mashhad University of Medical Sciences, from 2010 to 2011. After obtaining permission from the University's ethics committee and a written informed consent from each patient, we recruited 18 patients. The participants who had morbid obesity and were candidates for laparoscopic gastric bypass surgery were randomly allocated to two stapler and ligasure groups. The data were collected and analyzed by three statistical tests, including Mann-Whitney U test, by SPSS 16.Results: All patients were female with the age range of 20-65 years. Cost in the stapler group ranged between 29,500,000 to 40,000,000 Rial (mean 31,830,000± 3,500,000 Rials) and in ligasure group it was between 24,000,000 to 35,000,000 Rials (mean 26,720,000± 3,290,000 Rials). There was a significant difference between the two groups in cost (P=0.004(. Duration of the operations were 200±3.4 and 240±10 minutes in the stapler and ligasure groups, respectively. The difference in duration was significant between the two groups (P=0.043). No significant differences were observed in complications.Conclusion: Application of ligasure in resection and reconstruction of small intestine is more cost-effective than stapler, although duration of surgery is longer.