Background: One of the major complications after surgery is surgical site infection (SSI). The development of SSI is major cause of morbidity and mortality in surgical patients. Two indices of intrinsic infection risk have been proposed to predict SSI and to control for baseline differences among patients, allowing appropriate comparisons of infection rates: the Study of the Efficacy of Nosocomial Infection Control Index (SENIC) and National Nosocomial Infection Control Surveillance (NNIS) index. This would allow appropriate interhospital comparisons and a better use of infection rates as indicators of health care quality. Materials and methods: A prospective study conducted in the departments of Microbiology in collaboration with Surgical Gastroenterology. Total 816 patients were included in the study during April 2003 to Dec 2004. Epi info software is used for analysis. Results: 113 (13.9%) patients developed SSI. Both the indices have good explanatory and predictive power for the detection of SSIs in univariate analysis. To delineate whether the SENIC index added explanatory information to the NNIS index (or vice versa), we regressed each variable on the other. Logistic regression analysis confirmed the stratified analysis: residual of the NNIS index added discriminating ability to the SENIC index, whereas residuals of the SENIC index did not improve the predictive power of the NNIS index. Conclusions: The NNIS index had a better ability than the SENIC index for discriminating and predicting risk of SSI in gastrointestinal surgery.