Background and Purpose: Organ transplant recipients are vulnerable to fungal infections. The aim of this study was to determine the prevalence of fungal colonization and infections among patients who underwent various transplantations and molecularly characterize the etiological agents. Materials and Methods: This study was conducted on candidates for transplantation in Imam Khomeini Hospital, Tehran, Iran, from April 2017 to April 2018. All patients were monitored for fungal colonization or infections before and after transplantation. Isolated fungi were identified using molecular methods. Results: A total of 125 patients, including 86 males and 39 females, with the mean age of 52. 2 years participated in the study (age range: 15-75 years). Out of 125 patients, 84 (67. 2%) cases had fungal colonization that appeared pre-and post-transplantation in 21 and 63 cases, respectively (alone or concurrent with another infection in 55 and 29 cases, respectively). In addition, a total of 39 episodes of fungal infections were diagnosed in 36 (28. 8%) recipients (alone or concurrent with colonization in 7 and 29 cases, respectively). Out of the 39 fungal infections, 9 cases appeared pre-transplantation, while the other 30 cases occurred post-transplantation. However, no fungal colonization or infection was observed in 34 (27. 2%) patients. Oral candidiasis (n=20) was the most common type of infection, followed by funguria (n=7), onychomycosis (n=5), candidemia (n=3), rhinocerebral mucormycosis (n=1), cutaneous mucormycosis (n=1), cutaneous aspergillosis (n=1), and peritonitis (n=1). Six yeast species were recovered from colonization cases with the dominance of Candida albicans both before and after transplantation. The observed fungal infections were caused by 11 distinct species, including the members of Candida (i. e., C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and C. krusei), Aspergillus (i. e., A. oryzae and A. candidus), Rhizopus (i. e., R. oryzae and R. microsporus), Trichosporon asahii, and Trichophyton interdigitale. The results also indicated that the development of a fungal infection post-transplantation was associated with fungal colonization (r=0. 0184; P=0. 043). Conclusion: Based on the results, fungal colonization was a common finding in transplant recipients at Imam Khomeini Hospital. However, the incidence of fungal infections was comparable with those of other centers. As the oral cavity was the most common site of colonization and infection, it might be beneficial to take further care about the oral health of patients using effective mouthwash.