Presence of chromosomal anomalies is well known to be associated with reproductive failures where the incidence of chromosomal translocations is higher. Y:1 chromosomal translocations are reported to be rare and may have variable phenotypic effects such as infertility amongst others. The patient presented with azoospermia and dyslipidemia and coronary arterial disease. Cytogenetic tests such as karyotyping revealed the translocation, and fluorescent in situ hybridisation was performed to investigate the presence or absence of SRY gene. The SRY gene was found to be located on the p arm of the derivative Y chromosome. The test for Y chromosome microdeletions was reported to be negative for the AZF gene regions tested. Here we report the first case of Y:1 chromosomal translocation involving the break points (q11.2;p21) from India.