Background: Structural abnormalities of Y chromosome are commonly described in associated with the occurrence of a 45,X/46,XY chromosomal mosaicism. In recent years, evidences of an association between Y chromosome microdeletions and 45,X/46,XY mosaicism had been investigated, and 45,X/46,XY mosaicism was found to be particularly common in patients with Y chromosome microdeletions. The aim of our study was to investigate the presence of 45,X/46,XY mosaicism carrying a structurally abnormal Y chromosome in patients with Y chromosome microdeletions.Results: A 8-year retrospective study was conducted on 6545 infertile men with nonobstructive azoospermia or oligozoospermia. A total of 19 patients with 45,X/46,XY mosaicism or its variants were found, of which 78.95% (15/19) had a structural Y chromosome abnormalities in 46,XY cell line. Thirteen of 19 (68.42%, 13/19) patients with 45,X/46,XY mosaicism had Y chromosome microdeletions, and 12/13 (92.31%) of them exhibited a structurally abnormal Y chromosome.Conclusions: Our results were consistent with previous studies that a high frequency of 45,X/46,XY mosaicism or its variants were detected in patients with Y chromosome microdeletions. Different from previous studies, we found that 45,X/46,XY mosaicism in patients with Y chromosome microdeletions almost all exhibited a structurally abnormal Y chromosome.