Philippines is an archipelago in the Western Pacific Ocean. It is one of the most populated country in Southeast Asia, harboring multiple ethnic groups and cultures. Most of the non-indigenous population is composed by Chinese and Spanish immigrants. In order to characterize the Y-STR composition of Philippines, in the present study, we have collected 74 samples from unrelated males from the three main geographical divisions: Luzon, Visayas and Mindanao. These samples were typed for the 27 Y-STR loci included in the YFiler Plus kit. A high Y-STR haplotype diversity was found with all haplotypes being unique in our sample. Low diversity values were found for DYS391 and DYS438 (below 34%) and the multi-loci markers DYS385 and DYF387S1 were among the most diverse ones (above 95%). Since no data is available for the full set of YFiler Plus markers, a smaller set was used to calculate genetic distances between Philippines and other Southeast Asian populations. The results showed no significant differences between our samples and two other samples from Philippines, one from the general population and the other restricted to Luzon region. Significant differences were observed when comparing any of the three Philippines samples with Vietnam and Singapore populations.