Y chromosome microdeletions in the azoospermia factor (AZF) locus have been associated with spermatogenic failure. The frequency of AZF deletions is estimated to be about 10-18% in subgroups of idiopathic azoospermia and severe oligospermia, whereas the deletion frequency is estimated to be about 1.5-10.6% in the general population. Patient selection criteria as well as experimental and study design are the major factors that influence the deletion frequency. We designed a nation-based population screening with a well-defined study and experimental criteria to answer, first, what is the deletion frequency in a study population of high risk for Y deletion in the Greek-Cypriot origin and second, if there are any differences in the deletion frequency in the investigated specific subgroup of patients from different geographic/ethnic origin. Eighty Greek-Cypriot patients who met the selection criteria were included in this study as well as 50 fertile control males. The sample size is quite large when compared with the size of the population. All samples were collected from all districts of the island of Cyprus as the population is of the same religious, geographic and ethnic origin. All patients and controls had detailed clinical information and at least two semen-analysis reports based on World Health Organization standards. Samples with abnormal karyotypes, obstructive azoospermia or oligospermia with >2 x 106/mL were excluded from this study. The experimental design required a referral team and laboratory to undertake the responsibility to collect all the samples, all clinical and laboratory information, isolate DNA and carry out all tests, data analysis and interpretation. In our study, Y chromosome microdeletions have been found in patients with spermatogenic failure. Under the specific patient selection criteria and experimental design, the overall frequency is 5%, while among azoospermic patients it is 12.5%. In the subgroups of patients with idiopathic cause it is 5.9% and in idiopathic azoospermia it is 14.3%. No variation in the overall deletion frequency or the specific subgroups deletion frequency were found, as compared with frequencies found in patients from different geographic/ethnic origin.