The rising burden of opportunistic invasive fungal diseases (IFD) has been evolving for the past two decades in Uganda. In Uganda, HIV/AIDS has highlighted cryptococcal meningitis as a leading IFD with a high mortality rate where 10-week survival rates after cryptococcal meningitis are <50% in routine care. However, the incidence of other IFDs is not known. The cross-sectional study will be conducted in Mulago National Referral Hospital, Lacor and Lira Hospitals. Blood culture retrieved fungal isolates will initially be identified to species level using the standard algorithm for identification. Antifungal susceptibility testing will be performed using the EUCAST methods. Polymerase chain reaction assays will be used to type Cryptococcus species isolates from the patient’s blood and environment. Mycetoma granules from patients who present with the features of mycetoma will be assessed by direct microscopy and culture for diagnosis. Findings from this study will be important in providing baseline information on the epidemiological trend of IFDs in Uganda for patient management and research.