Background: Chromosomal aberrations are one of the most common causes of mental retardation (MR). Objectives: In this study, in order to identify the rate of chromosomal abnormalities in idiopathic MR, 50 MR patients at a charity center in Hamadan, Iran, were investigated. Methods: Fifty mentally retarded male patients without specific chromosomal abnormalities (e.g., Down syndrome, Fragile X syndrome, and Klinefelter syndrome) were included in the study. Standard cytogenetic techniques and high resolution GTG banding were performed on all the patients. Results: All the patients were male, with a mean age of 37.12 years. Skeletal and facial abnormalities were found in 8% and 22% of patients, respectively. All the patients showed a moderate to severe level of mental retardation. None of the patients had numerical chromosome abnormalities. Two out of the 50 patients (4%) demonstrated structural chromosomal abnormalities. One patient had a paracentric inversion in chromosome 1, while the other had a pericentric inversion in chromosome 2. Conclusions: The presence of structural chromosomal abnormalities (4%) in the studied MR patient population emphasizes the importance of cytogenetic investigation for all idiopathic MR patients.