The Y chromosome has been suggested to play a role in prostate cancer (PCa) because the loss of this chromosome is the most common aberration in PCa. Study of short tandem repeats (STRs) could provide a means to rapidly scan genomes at known or unknown predisposing loci for some diseases. DNA samples from 281 patients with PCa at the Portuguese Institute of Oncology, Porto, Portugal, and a population control of 175 healthy controls were analyzed for region Yp11.2 using AmpFlSTR Y-Filer kit (Applied Biosystems). The results demonstrated that microvariant alleles of DYS458 are overrepresented (p = 0.026). We found that allele 12 of DYS393 and allele 19 of DYS458 could have a protective effect (p = 0.0051; odds ratio [OR] = 0.48; 95% confidence interval [95% CI] 0.27-0.38; and p = 0.0272; OR = 0.47; 95% CI 0.22-0.98). On the other hand, patients carrying allele 13 of DYS393 presented an increased risk to PCa (p = 0.015; OR = 1.97; 95% CI 1.26-3.07). These results are in concordance with the involvement of Y chromosome in PCa development. STR allele studies may add further information from the definition of a genetic profile of PCa resistance or susceptibility. As TSPY is located at region Yp11.2, this gene could play an essential role in PCa development.