Natural Orifice Translumenal Endoscopic Surgery (NOTES) is a recent emerging technique for performing general surgery procedures such as cholecystectomy (gallbladder removal). However, the advantages of NOTES over conventional laparoscopic surgery, the current gold standard, are still questionable. The aim of this study was to show the impact of introducing new surgical instruments in the NOTES technique on surgical performance in a cholecystectomy as compared to conventional laparoscopic surgery. A set of videos from real cholecystectomy cases performed using these two different techniques were analyzed. Hierarchical task decomposition and timeline analysis were conducted for each technique. A comparison to show variations between the two techniques at the task level is presented to highlight the technical issues, and their effects on performance, associated with the use of current endoscopic tools in the NOTES technique. The results show a longer procedural time in the NOTES technique than in the laparoscopic technique with the highest increase in surgical time for dissection tasks. The tools used for dissection were also shown to be inadequate for the task based on the motion analysis. Using this systematic method of analysis, new surgical techniques can be assessed based on performance measures, while areas of design improvement in surgical tools can be identified and related to the performance assessment.