The recurrence of underlying diseases remains a major cause of graft failure after liver transplant. This study aimed to identify factors associated with the recurrence of underlying diseases and investigate the incidence of these factors and recurrence at the main liver transplant center in Iran. We included adult liver transplant recipients followed at Shiraz Transplant Center between 2011 and 2018 with a confirmed diagnosis of recurrence of underlying disease in our study. We reviewed medical records and extracted data on demographic characteristics, clinical and paraclinical features, medication use, and current status. We used a systematic random sampling method to select a control group of 95 transplant recipients who did not have recurrence. Of 3022 total transplant recipients, 76 recipients experienced a recurrence of their underlying disease. Model for End-Stage Liver Disease score, underlying disease, recipient blood group, donor sex, donor blood group, and rejection frequency were significantly different between study groups with and without recurrence of underlying diseases. Liver transplant recipients with recurrence had lower mean Model for End-Stage Liver Disease score. Recipients with recurrence also had higher rate of drug consumption (eg, prednisolone, tacrolimus, mycophenolate mofetil, sirolimus). Regression analysis showed that donor sex and rejection frequency had an effect on disease recurrence. Death occurred more frequently in liver transplant recipients with recurrence than in the control group (39.5% vs 26.3%), butthe difference was not significant. Donor sex and acute rejection frequency are independent factors predictive of the recurrence of underlying disease. Modifying risk factors can help minimize the recurrence of underlying diseases after liver transplant.