As a World Health Organization (WHO) guidelines, infertility is the couple’s inability to conceive after 2 years of regular unprotected intercourse. The investigation in male infertility is assuming greater importance because approximately half of all infertility cases caused by male factors. Although previous studies suggest that many cases with male infertility have a genetic and environmental etiology to the condition, and the majority of cases are idiopathic. About 10-20% of azoospermic patients are showing the microdeletion in Y-chromosome. In this deleted region, azoospermia factor (AZF) locus which is located in the Yq11 divided into the four regions as AZFa, AZFb, AZFc, and AZFd. In each of these regions a particular testicular histology and candidate genes have been found. The deleted in azoospermia gene family is also the most frequently deleted in AZFc region. Recently, not only Y chromosome, but X chromosome and some autosomal genes are also found in respect to male infertility. Frequent attacks on the naked mitochondrial DNA of sperm will responsible for oxidative damage or mutation to the mitochondrial genome and lead to male infertility. The introduction of molecular techniques, such as intracytoplasmic sperm injection, genomics, proteomics, metabolamics, has provided great perception into the genetics of infertility. Still our understanding to find a correlation between genotype and phenotype in male infertility remains limited. © 2014 All Rights Reserved.