Two pathogenic CNVs, a 10q25.3-q26.2 and a 13q33.1 deletion encompassing the <i>FGFR2</i> and the <i>EFNB2</i> gene, were associated with genital atypia and syndromic characteristics in two patients with 46,XY DSD. This evidence concerns the gene FGFR2 and disorder of sexual differentiation.