Background: The aspects of the epidemiology of bloodstream Candida infections including clinical features, the causal agents, underlying conditions, and risk factors have not been well-defined in Iranian pediatric patients. The aim of this observational study was to identify uncommon Candida species isolated from blood and other normally sterile specimens of the neonates and children admitted to intensive care units at Children’ s medical center, Tehran, Iran. Methods: The studywascarried out prospectivelyonpatients< 16 years, whowere hospitalized in Children’ s medical center, Tehran, Iran, during 25 months, from June 2014 to July 2016. Blood and other normally sterile specimens were collected from 6, 075 pediatric patients and only pure growth of yeasts were included the study. The yeast isolates were subjected to DNA extraction, PCR of ITSregion, and sequencing followed by Blast analysis to accurately identify the species. Results: A total of 16 out of 136 isolates were recognized as uncommon or rare Candida species. According to the sequence analysis, these isolates were identified as C. orthopsilosis (N = 5, 3. 7%), C. glabrate (n = 4, 2. 5%), C. dubliniensis (n = 2, 1. 5%), C. lusitaniae (n = 2, 1. 5%), C. kefyr (n = 2, 1. 5%), and C. intermedia (n = 1, 0. 75%) Conclusions: Candida species, which were once considered harmless, havenowbeen recognized as causative agents of Candidemia. It is essential to consider, manage, and control the conditions that lead to the development of these unusual but severe cases of Candidemia.