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Objective: This investigation uses the comprehensive complication index (CCI) to compare complications after natural orifice transluminal endoscopic surgery (NOTES) procedures., Background: NOTES procedures are developed to miniaturize surgical trauma. NOTES publications inconsistently report complications. The CCI improves reporting of complications., Methods: The CCI is calculated using complication data from a single center, double blind, randomized controlled trial comparing transvaginal [transvaginal cholecystectomy (TVC), N = 41] and conventional laparoscopic cholecystectomy (CLC, N = 51). Complications are assessed using the classification of surgical complications (CSC). Two different scenarios are applied to the CSC for definition of complications with an emphasis on minor complications. CSC data are fed into the free online CCI-calculator. The CCIs from complication data from other NOTES reports are calculated accordingly and compared to our results., Results: The CCI allows easy indexing of complications with or without a CSC table. For scenario I, the mean CCI of CLC versus TVC is 3.3 (± 6.3; SD) versus 3.5 (± 6.4; n.s.) and for scenario II it is 7.6 (± 6.4) versus 6.5 (± 7.0; n.s.). The difference of the mean between the two scenarios is highly significant (p < 0.000). The mean CCIs of both groups and scenarios are below the CCI of 8.7 for a grade I CSC complication. Similar calculation of CCIs from other NOTES publications yields mean CCIs below 8.7 for the surgical procedures reported., Conclusion: The CCI results in a single, easily comparable complication index for surgical procedures whereas the CSC yields tabular results. A significant difference in interpretation occurs with variation in definition of complications. Average CCIs below a value of 10 describe low complication rates. Authors need to describe their definition of complications if using the CSC and the CCI. More emphasis should be given to reporting of minor complications. The use of the CCI for NOTES procedures will enable international comparison.