The human Y chromosome is known to be poor in genes with more than 50% of its sequence composed of repeated elements. SRY gene and several other genes on the Y chromosome have been implicated in germ cell development and male infertility. The heterochromatic region comprises distal Yq corresponding to Yq12. This region is assumed to be genetically inert and is variable in length in the normal population. It is mainly composed of two highly repetitive sequence families, DYZ1 and DYZ2, containing about 5000 and 2000 copies, respectively. It has long been known that the length of the heterochromatic region of the Y chromosome varies within the population. In our study, we aimed to investigate the rate of Yqh(+) and Yqh(-) cases in all of the male patients applied Firat Medical Center between 2000-2006. A total of 1392 male patients applied our Medical Genetics Laboratuary for cytogenetic analysis. Cytogenetic analysis were performed by standart methods. For each case at least 25 metaphases were evaluated. Thirty eight cases of all were Yqh(+) (2.73%) and four cases were Yqh(-) (0.28%). Main indications at these cases were infertility, recurrent abortions and mental retardation. In conclusion, infertile men with oligozoospermia and azoospermia presented a higher prevalence of chromosomal alterations, even though they did not show a phenotypical feature of a genetical disease. Y chromosome polymorphisms could be one of the unknown factors disturbing the spermatogenesis. Therefore, we suggest that karyotyping is needed in evaluating males for genetic counseling and chromosomal diagnosis.