Background & aims: The rate of mortality from Spontaneous Peritonitis (SP) in cirrhotic patients is still high despite the development of new antibiotic treatments and intensive hospital care. The coexistence of spontaneous fungal peritonitis (SFP) is almost entirely ignored health problem, because it is difficult to be diagnosed at an early stage by conventional culture-based methods. Therefore, this study was designed to employ PCR-based method in evaluating the prevalence of fungal infection in cirrhotic patients with peritonitis who failed to respond to the recommended therapy and to determine its association with in-hospital mortality. Subjects and Methods: A total of 80 cirrhotic patients admitted to the hospital with ascitis (June-2013 to April-2015) were followed in this study. Results: During hospitalization, 23 (42%) of patients had died although they received guideline-driven treatment. The demographics, clinical, hematological, and biochemical data were similar in both mortality and survival groups. However, the incidence of fungus infection was the only significantly elevated parameter in the mortality group than in the survival group (7/23;30% vs.0/32;0%, P = 0.0012). This fungal infection was significantly associated with SP drug resistance development (P = 0.007). Intriguingly, all the cases of fungal infection were detected by PCR-based method while culture-based diagnosis was able to detect the fungal infection in only 4 of these cases indicating a diagnostic sensitivity of 57%. Conclusion: Our results reflect a strong association between SFP and in-hospital mortality in cirrhotic patients with SP that may offer a coherent explanation for the antibiotic treatment failure in such patients. Prompt PCR-detection and antifungal coverage is warranted in these cases.