Double aneuploidy is considered a rare phenomenon. Herein, we describe a case of double aneuploidy 48,XXY,+21 in a neonate with congenital heart defects. The 28-day-old neonate male (23-year-old mother and 24-year-old father) was admitted to a neonatal intensive care unit owing to congenital heart disease. Echocardiography showed a complete atrioventricular septal defect with Rastelli type B and significant left ventricular failure, moderate atrioventricular valve regurgitation, right-sided heart failure, and preserved systolic function. Cytogenetic analysis of the newborn showed double aneuploidy 48,XXY,+21. The maternal karyotype was 46,XX,inv(9)(p11q13) and the paternal was 46,XY. Characteristics associated with Down syndrome are observed in newborns; on the other hand, children under 10 months of age and neonates may show little or no signs of the Klinefelter syndrome. According to this study, there seem to be differences between the frequency of congenital heart disease among patients with Down- Klinefelter and Down syndrome. At about 11 months of age, the child died after undergoing heart surgeries. The early cytogenetic study is important for better diagnosis and management of the disease.