The purpose of this study was to evaluate the association between CNVs in specific regions of LEPR, NEGR1, ARHGEF4, CPXCR1, and INS and in four intergenic regions (1p36.33b, 12q15c, 15q21.1a, and 22q11.21d) and obesity in Mexican children. Here, ARHGEF4 is linked to obesity due to melanocortin 4 receptor deficiency.