OBJECTIVES: Postoperative infections bring about an expansion of length of hospital stay (LOS) and extra medical costs. METHODS: We analyze the relationship between variations in antimicrobial prophylaxis (AMP) and extra medical costs in surgical patients with colorectal malignancies. Utilizing profiling administrative data, we analyzed 161 admitted patients between 2007 and 2009 to a university hospital. We classified the patients into two classes based on AMP duration: the control group (112) and the case group (49). Most patients from both groups were appropriately given AMP agents consistent with the guidelines of infection-related associations. RESULTS: The LOS of the control group (24.6 ± 12.1 days) was shorter than that of the case (49.4 ± 35.2) (p<0.05). Hospitalization charge of the control group (15130 ± 3930 USD) was lower than that of the case (23130 ± 1212) (p<0.05), but hospitalization charge per day of the control group (670 ± 160 USD) was higher than that of the case (530 ± 130) (p<0.05). Furthermore, 73 cases of the control group were given on the day of surgery till the first postoperative day, and 39 cases were given to the second and third postoperative days. LOS of the former (22.7 ± 9.5 days) was shorter than that of the latter (28.3 ± 15.5) (p<0.05). CONCLUSIONS: AMP agents in our hospital were found to generally given according to the recommended guidelines. It is important for the hospital administrators to quantify the additional costs on top of the primary diagnosis in order to properly deal with infection control and hospital management.