Abstract： Objective:To investigate the karyotype distribution and genetic effect in male children with Y chromosome variation.Methods:Routine peripheral blood lymphocyte culture, chromosome preparation, and G banding for karyotype analysis were done in 63 children who visited the Urology, Endocrinology and Genetic Counseling Clinics of Henan Children’s Hospital from May 2008 to October 2022 for language, motor developmental backwardness, mental retardation or genital abnormalities. When the Y chromosome heterochromatin region was abnormal or morphology was difficult to identify, the distribution of abnormal Y chromosome types and their resulting clinical effects were analyzed using C-banding and fluorescence in situ hybridization (FISH) techniques for verification.Results:There were 19 different karyotypes in 63 children with Y-chromosome abnormalities, and the most common aryotype was associated with Klinefelter syndrome. Among the 63 cases, 17 cases were found to have abnormal Y chromosome number, accounting for 27.0% of the abnormal karyotypes. There were 3 abnormal Y chromosome structures, accounting for 4.8% of the abnormal karyotypes. 10 cases of Chimerism, accounting for 15.9% of the abnormal karyotypes. There were 3 cases of disorder of sexual development (DSD) , accounting for 4.8% of abnormal karyotypes. Y chromosome polymorphism was found in 30 cases, accounting for 47.6% of the abnormal karyotypes. All of these 63 cases suffered from various types of genital dysplasia and varying degrees of mental retardation and so on.Conclusion:The abnormal karyotype and polymorphism of Y chromosome are the important reasons for the abnormal development of male gonad and fetal development. Cytogenetic examination was carried out to determine the etiology of these children, and corresponding medical intervention was carried out as soon as possible. At the same time, genetic counseling and prenatal diagnosis should be conducted to reduce the birth rate of children with defects.