Cryptic chromosome aberrations are a common cause of idiopathic mental retardation and multiple congenital malformations syndromes (MR/MCM). MATERIAL AND METHODS: This study describes results and compares three methods for detection of submicroscopic chromosome aberrations in 76 children with MR/MCM and normal routine G-banded karyotype. RESULTS: Cryptic chromosome aberrations were detected in 15 patients (19.7%): in 3 of 19 patients (15.8%) by subtelomeric fluorescent in situ hybridization (FISH), in 5 of 47 patients (10.6%) by Multiplex Ligation Dependent Probe Amplification (MLPA) and in 7 of 23 patients (30.4%) by array-Comparative Genome Hybridization (array-CGH). Seven deletions, four duplications and four complex rearrangements have been diagnosed in the present study. Six were de novo and 2 were inherited from a parent carrier of balanced translocation. DISCUSSION: We observed a slightly higher imbalance incidence compared to the literature. Among these aberrations there were well known syndromes as well as some rare variants. CONCLUSION: This study confirms the utility of molecular-cytogenetic screening in patients with MR/MCM. We suggest array-CGH as the most reliable technique with a high diagnostic yield.