BACKGROUND: Malaria is the second most frequent clinically suspected disease entity after acute respiratory tract infection in developing countries. Active malarial transmission occurs throughout the year, while aggressive out bursts of disease are seen mainly during and after the 'monsoon' season. This study aimed to determine the morbidity and mortality associated with malaria during flood at Isra University Hospital, Hyderabad. METHODS: This prospective observational study was done at Isra University Hospital Hyderabad during monsoon flooding from July 2011 to October 2011. All 883 patients presented with symptoms of malaria (fever, headache, and vomiting) were evaluated and diagnostic tool ICT-MP was used for the detection of malaria parasite among them. RESULTS: Seventy four (8.38%) patients diagnosed for malaria. The mean age and SD was 30.11 +/- 1.67 years. Overall mortality due to malaria observed (18.9%). Mortality rate significantly observed high in pregnant women (0.005) and in those patients who developed complications such as, pneumonia (P = 0.04), renal failure (P = 0.04), Unconsciousness (P = 0.001), and Septicemia (P = 0.001). CONCLUSION: A Significant increase in the morbidity and mortality in patients with malaria after flood noticed. The probability of getting poor outcome is also associated when patient develop complications.