This study compared the management, prognostic factors and outcomes of patients with emphysematous pyelonephritis (EPN). Twenty-one patients with EPN were studied between September 1996 and August 2005, and were assigned to two groups. Patients in Group 1 received conservative treatment with/without percutaneous catheter drainage (PCD) while patients in Group 2 underwent nephrectomy following medical treatment and PCD. A post hoc analysis of the prognostic factors was performed between survivors and nonsurvivors, and between the survivors in Group 1 and Group 2. There were 14 patients in Group 1, and seven in Group 2. The mortality in Group 1 was 35.7% (5/14) and in Group 2 was 0% (p = 0.12). There were no statistically significant differences in prognostic factors between the two groups, though patients in Group 1 had relatively lower platelet counts (p = 0.07) and Group 2 patients had a higher incidence of dialysis after nephrectomy (p = 0.03). Comparing the survivors and nonsurvivors, patients with comorbid congestive heart failure and patients initially presenting with consciousness disturbances had higher mortalities (p = 0.02 and p < 0.01, respectively). Nonsurvivors also had lower platelet counts (p = 0.06). In conclusion, medical treatment with/without PCD can be used to manage patients with EPN. More agressive drainage is needed in patients with congestive heart failure who initially present with consciousness disturbances or thrombocytopenia.