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Purpose: To detect incidences and the types of chromosomal abnormalities in Chinese men with infertility and determine chromosomal factors association with various phenotypes. Methods: Semen analysis and karyotype analysis by G-banding were carried out in 4,659 idiopathic infertile males; additionally, multiplex PCR using nine specific sequence-tagged sites (STSs) was used to detect azoospermia factor (AZF) microdeletions in 412 patients with Y chromosomal abnormalities. Results: Male infertility was divided into pregestational infertility, characterized by failure to produce a fertilized ovum, and gestational infertility, characterized by embryo loss after fertilization. The former can result from azoospermia, oligozoospermia or oligoasthenozoospermia syndrome, while the latter is associated with developmental early pregnancy loss, habitual miscarriage and stillbirth. Among 4,659 male patients, 412 (8.84 %) showed abnormal chromosomal karyotypes, including 314 (6.74 %) with sex chromosomal abnormalities and 98 (2.10 %) with autosomal abnormalities. The prevalences of numerical and structural abnormalities among patients with chromosomal abnormalities were 259/412 (62.86 %) and 153/412 (37.14 %), respectively. Furthermore, structural sex chromosomal abnormalities were represented by various phenotypic profiles (46,XX, 47,XYY and 45,X/46,XY), and a prevalence of AZF microdeletions of 19/79 (24.05 %). AZF microdeletions were highly associated with Y chromosomal abnormalities ( P = 0.018). Conclusion: Various chromosomal abnormalities that result in male infertility could affect spermatogenesis or embryonic development at different levels. Sex chromosomal and autosomal abnormalities were highly associated with pregestational and gestational infertility, respectively. AZF microdeletions may play an important role in lowering the stability of the Y chromosome. [ABSTRACT FROM AUTHOR]