Prostate cancer is a significant disease in men and a large number of individuals would benefit if risk factors that increase the susceptibility to develop this neoplasia could be established, which could aid in the early detection of the disease that is crucial for successful treatment. The first objective of this study was detection of allelic frequencies of 17 Y-chromosome short tandem repeat loci from Iraqian prostate cancer patients and normal control males. The second objective was evaluating the association of these loci with the presence of prostate cancer. Blood samples were collected from 100 unrelated male patients living in Middle and South of Iraq. FTA® Technology was utilized to extract DNA from blood collected on FTA™ paper. One 1.2 mm punch from a card containing whole blood was loaded into the appropriate wells of the reaction plate. The PCR was realized with the GeneAmp® PCR System 9700 thermal cycler. Post PCR amplification was detected using an ABI Prism1 3130xl Genetic Analyzer 16-capillary array system, with POP-7™ Polymer and Data Collection Software, GeneMapper version 3.5. Six alleles (20 to 25) for DYS635, three alleles (14 to 16) for DYS437, five alleles (18 to 22) for DYS448, five alleles (13 to 17) for DYS456, seven alleles (14 to 20) for DYS458, five alleles (10 to 14) for YGATA H4, three alleles (12 to 14) for DYS389I, six alleles (28 to 33) for DYS389II, five alleles (13 to 17) for DYS19, five alleles (8 to 12) for DYS391, four alleles (9 to 12) for DYS438, five alleles (21 to 25) for DYS390, six alleles (9 to 14) for DYS439, four alleles (11 to 14) for DYS392, three alleles (13 to 15) for DYS393, eight alleles (11 to 19) for DYS385a and eight alleles (13 to 20) for DYS385b were found among the whole Iraqi subjects examined. A higher incidence of disease was found among males who had either allele 10 of DYS391 or allele 13 of DYS393. It is likely that Iraqi males who belong to Y-lineages with either allele 10 or allele 13 are more susceptible to develop prostate cancer, while those belonging to lineages with allele 9 and 14 of DYS439 or allele 15 of DYS385b are more resistant to the disease. This study shows the influence of genetic factors on prostate cancer, and it seems that DYS391 and DYS390 loci comprising DYS635, DYS437, DYS448, DYS456, DYS458, YGATA H4, DYS389I, DYS389II, DYS19, DYS438, DYS439, DYS392, DYS393, DYS385a and DYS385b STRs have the potential to be used as a screening method for prediction of susceptibility to prostate cancer in Iraqi population.