The evaluation of multiple congenital abnormalities and/or mental retardation (MCA/MR) is always a challenge to clinicians. The recognition of specific physical or behavioral characteristics can vastly improve diagnostic yield. Chromosomal abnormalities account for a high percentage in the etiology of MCA/MR. In this study, frequency of chromosomal abnormalities was 4.81% of 457 patients. Chromosomal abnormalities and polymorphisms were detected in 65 (14.21%) (structural and numerical chromosomal abnormalities in 22 patients and polymorphisms in 43) of 457 MR and/or MCA patients. Our results show that chromosomal abnormalities contribute much to the causation of multiple malformations and/or MR. It is essential that fluorescence in situ hybridization (FISH) be used in conjunction with standard methods in order to maximize obtainable information for better management of patients with MR and/or MCA.