Apparently balanced de novo structural chromosome rearrangements (ABCR) are associated in around 6– 23 % cases with abnormal phenotype, depending on type of the anomaly. Several mechanisms were proposed to explain the clinical phenotype, such as submicroscopic genomic imbalances, gene disruption at or near the breakpoints or position effect, which could not be diagnosed by using classical cytogenetic and molecular cytogenetic techniques. The array-based comparative genomic hybridization (a-CGH) is an efficient tool to detect the possible gains and losses not only at the breakpoints but also in the whole genome. We report here, a-CGH findings of 20 apparently balanced de novo rearrangements detected in three prenatal and 17 postnatal cases with abnormal phenotypes. Identified rearrangements were 13 reciprocal translocations, two inversions and five complex chromosomal rearrangements (CCRs). Genomic imbalances were found in eight cases (40 %) by using a-CGH technique. Seven imbalances were at the breakpoints of the rearrangements while one was located on unrelated chromosome. An imbalance was observed at the breakpoints in five of the 13 translocations (38,5 %), in one of the two inversions (50 %) and in one of the five CCRs (20 %). In one case with CCR showed a 2.5 Mb deletion at 11p14.1- p13, which was compatible WAGR syndrome. Clinical and laboratory findings of these cases will be presented in detail.