The 49, XXXXY syndrome was first reported in 1960. It represents a rare sex chromosome aneuploidy syndrome. Some consider it as the most severe variant of Klinefelter syndrome (47, XXY). The approximate incidence is 1 in 85,000 male births. The karyotype arises from maternal non-disjunction during both meiosis I and meiosis II. The clinical presentations of 49, XXXXY syndrome include mental deficiency, hypogonadism, severe speech delay, multiple skeletal anomalies, cardiac defects and characteristic facial features. It might be mistaken for Down syndrome and needs chromosome analysis for confirmation. According to literature review, urinary tract anomaly in association with 49, XXXXY syndrome was extremely rare. Here we report a case of 49, XXXXY with Down syndrome-like facial dysmorphism, who was found to have patent ductus arteriosus and hypotonia. Moreover, he also got grade V vesico-ureteral reflux, R't with hydronephrosis and urinary tract infection. We hope to remind clinicians to arrange chromosomal analysis if multiple congenital anomalies exist in a neonate. And remember to exclude congenital genitourinary tract anomaly if karyotype 49, XXXXY is diagnosed.