Y Chromosome Microdeletions test is recommended when men are either Azoospermic or severely oligozoospermic (sperm count < 5 x 3^{^}10⁶/ml). Six common deletion sites are screened in the 3 AZF regions a, b and c; these are:

1. SY84
2. SY86
3. SY127
4. SY134
5. SY254
6. SY255

Y Chromosome Microdeletions by PCR is performed at biolab Molecular Genetics Department as per the Clinical Molecular Genetics Society (CMGS) Best Practice Guidelines. Multiplex polymerase chain reaction (PCR) is used, followed by gel electrophoresis. Analytical sensitivity and specificity are 99 percent.

Sex determination (controlled by the SRY gene) has long been viewed as the sole function related to the Y chromosome, but this theory changed in recent years when another important function (the control of spermatogenesis) was discovered and many genes were mapped to the Y-chromosome.

Spermatogenesis is the process of sperm cell development. Rounded immature sperm cells undergo successive mitotic and meiotic divisions (spermatocytogenesis) and a metamorphic change (spermiogenesis) to produce spermatozoa.

Spermatogenesis loci termed Azoospermia Factors (AZF) AZFa, AZFb, and AZFc, are located on the long arm of the Y-chromosome (Yq11.21-23). A microdeletion in one or more of these AZF loci is the most common cause of male infertility. Moreover, infertility is a major health problem affecting 10–15% of couples seeking to have children, and a male factor can be identified in about half of these cases. A significant proportion of infertile males are affected by either oligozoospermia (reduced sperm production) or azospermia (lack of any sperm in the ejaculate).

Generalized genotype/phenotype correlations are possible for common microdeletions. Their frequencies have been estimated:·         AZFa deletion: spermatogenic failure (Sertoli-cell-only syndrome, SCOS) resulting in azoospermia; 5 percent of cases.·         AZFb deletion: azoospermia/spermatogenetic arrest; 10 percent of cases.·         AZFbc deletion: SCOS/spermatogenic arrest; 13 percent of cases.·         AZFc deletion: variable phenotype ranging from mild oligospermia to azoospermia and SCOS; 70 percent of cases.·         AZFabc deletion: SCOS associated with azoospermia; 2 percent of cases.