Background: Differences of sex development (DSD) is a group of heterogeneous conditions with a diverse pathophysiology. They are generally characterized by an abnormality of the chromosomal, gonadal or phenotypic features that typically define sex development. Aim: The study aim was to introduce Multiplex ligation-dependent Probe Amplification (MLPA) technique in the diagnostic workup of 46,XY DSD patients and to correlate genotypic abnormalities with clinical phenotype for more understanding of etiologic background. Methods: The study was carried out on thirty five 46,XY DSD patients selected from the Endocrinology clinic, Institute of human genetics and genome research, National Research Centre, Egypt. Patients underwent thorough clinical examination, hormonal assessment, pelvic ultrasonography and genitography. Laparoscopy with gonadal biopsy and histopathological evaluation were done when indicated. All patients were subjected to karyotype and MLPA analysis. Results: Clinically significant Copy number variations (CNVs) were detected in three patients in the form of SOX9 gene deletion in 2 patients, deletion of DMRT1 in 1 patient, while heterozygous duplication (of unknown significance) in HSD17B3 gene was detected in 1 patient, with an overall rate of 11.4%. Conclusion: MLPA is a robust cost-effective technique for screening of 46,XY DSD patients as a complement to Sanger sequencing. CNV analysis should be added to the first-line diagnostics in 46,XY DSD, especially if the phenotype includes malformations in other systems.