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Male factor infertility often happened in patients with varicocele and genetic disorder.Microsurgical varicocele is the most effective and safe treatment option for male infertility in patients with varicocele.Y chromosome microdeletions and chromosomal abnormalities are the two types of genetic disorder.Now we could use commercial detection kits through PCR amplification of selected regions of the Y chromosome.In this report,I will introduce the application of Y chromosome microdeletions analysis in clinical reproductive dysfunction.