Introduction: Aneuploidies are frequent genetic disorders on clinical practice; nevertheless, the knowledge about how other genetics variants could influence on final phenotype is no very precise. Objective: To determine copy number variations and regions of homozygosity greater than 0,5% or larger than 10 Mb in newborns with autosomal aneuploidies. Materials and methods: We performed chromosomal microarray analysis to the newborns with autosomal aneuploidies (n=7), trisomy 21 (n=5) and trisomy 18 (n=2) evaluated at the Hospital Antonio Lorena and Hospital Regional of Cusco-Perú in 2018. Result: In two neonates we found pathogenic and probably pathogenic copy number variants in other genomic regions different to chromosomes 21 or 18. Furthermore, we found two uncertain significance variants bigger than 500 kpb. Conclusions: The number of individuals analyzed was small; but is important to stand out that we found that almost half of them, had others copy number variants associated to neurodevelopment disorders, congenital anomalies, deafness, short/tall stature and another with negative influencing in phenotype in patients with aneuploidies.