We investigated a group of 376 children, seen over a period of 7 years with different types of congenital cardiovascular defects, to assess the presence of chromosomal aberrations. The diagnostic approach, achieved in 3 consecutive steps, revealed conventional chromosomal aberrations in 30 of the patients (8%) excluding trisomies 13, 18, 21. Fluorescence in situ hybridisation for microdeletions showed 51 microdeletions (15%), with 43 patients having deletions of 22q11.2, 7 patients with deletion of 7q11.23, and 1 patient with deletion of 4p16.3. In 23 patients with additional clinical abnormalities, we carried out a subtelomeric screening. This revealed, in two cases (9%), different subtelomeric aberrations, namely deletions of 1p and of 1q. Thus, subtelomeric screening proved to be a very valuable as a new diagnostic approach. Our approach to genetic investigation in three phases makes it possible to detect a high rate of pathologic karyotypes in patients with congenital cardiovascular malformations, thus guaranteeing more effective genetic counselling of the families, and a more precise prognosis for the patient.