Background: Congenital heart disease (CHD) is the most common disorder among live births with an incidence of 10/1000 newborns. It is also considered a major cause of morbidity and mortality. In most cases, the cause of CHD is multifactorial with a genetic background. Aim of Study: The objective of this work was to improve the diagnostic outcome among children with CHD associated with other somatic anomalies or developmental delay by using Multiplex Ligation Dependent Probe Amplification (MLPA) technique. Patients and Methods: Forty patients with CHD and extra cardiac manifestations were examined using conventional cytogenetic analysis and MLPA Microdeletion and Subtelomere kits. Chromosomal microarray (CMA) was carried out for three patients with normal MLPA results. Results: MLPA analysis showed abnormalities in 5 patients (12.5%) in the form of Williams-Beuren, 22q11.2 microdeletion or DiGeorge (DS), Wolf -Hirschhorn and 2p25.3 microduplication syndromes. CMA showed an interstitial 2.27 Mb deletion of chromosome 2q22 including the entire ZEB2 gene in one patient with characteristic facial features who was accordingly diagnosed as Mowat Wilson syndrome. Conclusion: The present study markedly increased the diagnostic yield of patients with CHD associated with other somatic anomalies and detected two rare patients, one with atypical 2p25.3 microduplication and the other with Mowat Wilson syndrome. The conduction of larger analytical studies using different molecular cytogenomic techniques including CMA on a larger scale is recommended to provide better understandings of gene implication and improve the diagnostic and prevention strategies of CHD.