Sepsis is one of the most important causes of morbidity and mortality in patients presenting to the emergency department. SIRS criteria that define sepsis are not specific and do not reflect the severity of infection. We aimed to evaluate the ability of the modified mortality in emergency department sepsis (MEDS) score, the modified early warning score (MEWS) and the Charlson comorbidity index (CCI) to predict prognosis in patients who are diagnosed in sepsis. We prospectively investigated the value of the CCI, MEWS and modified MEDS Score in the prediction of 28-day mortality in patients presenting to the emergency department who were diagnosed with sepsis. 230 patients were enrolled in the study. In these patients, the 5-day mortality was 17 % (n = 40) and the 28-day mortality was 32.2 % (n = 74). A significant difference was found between surviving patients and those who died in terms of their modified MEDS, MEWS and Charlson scores for both 5-day mortality (p < 0.001, p = 0.013 and p = 0.006, respectively) and 28-day mortality (p < 0.001, p = 0.008 and p < 0.001, respectively). The area under the curve (AUC) for the modified MEDS score in terms of 28-day mortality was 0.77. The MEDS score had a greater prognostic value compared to the MEWS and CCI scores. The performance of modified MEDS score was better than that of other scoring systems, in our study. Therefore, we believe that the modified MEDS score can be reliably used for the prediction of mortality in sepsis.