Invasive fungal infection has become the leading cause of death after transplantations. Serious fungal infections may cause 5-10% of deaths in those undergoing lung, pancreas or liver transplantation. The aim of the present study was to identify the incidence of invasive fungal infections in solid organ transplant recipients, in Nemazi hospital, Shiraz University of Medical Sciences, Shiraz, Iran. Recipients undergone liver and kidney transplantations were followed for fungal infections for a minimum 6 month period. All clinical samples were examined by routine methods. Whole blood specimens were collected prospectively once per week and were evaluated for any invasive fungal infections by panfungal PCR and PCR-Enzyme Link Immunosorbent Assay (ELISA). One handrad-sixty eight recipients were transplanted between September 2004 and January 2006 (75 females, 93 males, mean age:34.4 years), In proven and probable recipients for fungal infections, the sensitivity, specificity, positive and negative predictive values by panfungal PCR-ELISA were 83.3%, 91.7%, 76.9% and 94.3% ,respectively. By PCR-ELISA, fungal infections were diagnosed in 14 recipients (8.3%). Time of infection in blood prior to any clinical signs was 7-70 days with mean of 21.4 days. The etiologic agents were Candida albicans (13 recipients) and Aspergillus fumigatus (1 recipient).Of the 14 cases, eleven recipients died. Fungal infections are associated with increased morbidity and mortality rates following transplantation. Treatment strategies involving antifungal prophylaxis for high risk patients and earlier initiation of antifungal therapy in cases of presumed infection are warranted.