Objective: Chromosomal abnormality is the cause of a substantial proportion of dysmorphic/mental retardation syndromes. Cryptic rearrangements less than one chromosomal band stayed unrecognized. The method of fluorescent in situ hybridization (FISH) provides a possibility for identifying imbalanced chromosomal changes. Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements and identification of marker and derivative chromosomes. Careful selection of patients with a specific set of dysmorphic signs is a prerequisite for a successful analysis. Materials and methods: In this study we applied FISH microdeletion probes in the diagnosis of 2 patients with Prader-Willi Syndrome [del(15)(q11.2q)], 3 patients with DiGeorge syndrome [del(22)(q11.2q)] and 7 patients with Williams syndrome [del(7)(q11.23q)]. Dysmorphic features, neuro-psychological profile and major anomalies were studied prior to the analysis and were compared with these described in the literature. Metaphase spreads were obtained from peripheral blood lymphocytes. Appropriate FISH probes according the standard procedure were used for each case. Microdeletion was confirmed using fluorescent microscope. Discussion: All the cases meet the criteria for these specific syndrome- cases with Williams syndrome had specific cardiac anomaly of the aorta or pulmonary artery, elfin face, characteristic behavior and hypercalcemia; Prader-Willi patients were obese with short stature, hypogonadism and small hands; the main feature in DiGeorge patients was cardiac anomaly accompanied with palatal cleft, micrognathia and prominent nose. All of them had moderate mental retardation. Conclusion: Cytogenetic analysis should always be supplemented with FISH to diagnose all cases suspected for a microdeletion syndrome. Providing the useful diagnostic information is important for genetic counseling and prognosis of these syndromes.