Objectives To estimate the incidence rate of fungal infections after hepatobiliary surgery and identification of the risk factors. Background Candidemia and disseminated candidiasis are major causes of morbidity and mortality in hospitalized patients, especially in the ICU, the incidence of invasive candidiasis is on a steady rise because of increasing use of multiple antibiotics and invasive procedures carried out in the ICUs. Participants and methods A prospective cohort hospital-based study was carried out at the National Liver Institute, Menoufia University. The studied group was 210 patients, all of them were examined thoroughly, their data were registered and sampled two times, one at the day of admission to be sure that they are free of fungal infection and the second was after hepatobiliary surgery. A predesigned questionnaire was used, which includes data about personal history, medical history, and suggested risk factors for fungal infections. Results In the present study, the incidence rate of fungal infection among patients who had hepatobiliary surgeries in National Liver Institute was found (45.2%) and by logistic regression analysis of data indicated that the most relevant factors for fungal infection were age (P < 0.001), antibiotic use (P < 0.05), liver disease (P < 0.05), central venous catheter (P < 0.05), urinary catheter (P < 0.05), and ICU hospitalization more than 48 h (P < 0.001). Conclusion High incidence of fungal infection after hepatobiliary surgeries is considered a great health problem. The main risk factors of fungal infection are low immunity, chronic disease, diabetes, hepatitis B virus and/or hepatitis C virus infection, cancer, anemias, organ transplantation, blood transfusion, had central venous catheter, intravenous catheter, had abdominal drain, urinary catheter, parenteral nutrition, history of past operations, and hospitalized in the ICU more than 48 h.