Objective To compare the APACHE Ⅱ score, SAPS Ⅱ score and SOFA score in determining whether there is infection in critically ill patients and prognostic assessment. Methods The patients involved in this study were recruited from surgical intensive care unit (SICU), respiratory intensive care units (RICU) and emergency intensive care unit (EICU) of Chinese PLA General Hospital from October 2012 to December 2012. All of the clinical data were collected during hospitalization. According to pathogenic examination results, the patients were divided into non-infected group and infected group. Based on 28-day survival, the patients were further divided into surviving group and the dead group. Diagnostic performance curves were employed to compare APACHE Ⅱ, SAPS Ⅱ and SOFA scores. Results The study included 156 cases of ICU patients. The APACHE Ⅱ and SAPS Ⅱ score in patients with infection were higher than those of non-infected patients (14.7±9.1 vs 11.8±9.0, P=0.07; 33.1±18.4 vs 26.8±19.1, P=0.048). The area under the curve of SAPS Ⅱ score used in the diagnosis of infection was 0.641. When this score> 15, the sensitivity for the diagnosis of infection >80%. APACHE Ⅱ, SAPS Ⅱ and SOFA scores in dead group were higher than those in the surviving group (23.9±6.6 vs 11.0±7.1; 49.8±18.9 vs 26.4±13.3; 9.4±3.6 vs 3.2±2.8, P all<0.001). According to diagnostic performance under ROC curve analysis, SOFA score had the largest area under the curve (AUC=0.907). When the SOFA score reached 5.5, sensitivity rate for bad prognosis was 86.7%, specificity rate was 88%. Conclusions SAPS Ⅱ score can suggest the presence of infection; while SOFA score can indicate poor prognosis of patients.