The purpose of this study was to compare the morphology/morphometry and fertilizing capacity of human spermatozoa recovered via swim-up method, Percoll density gradient method, and SpermPrep'@II filtration method. Thirty-three ejaculates were equally divided into 2 aliquots. Aliquot 1 was processed via the direct swim-up method, whereas aliquot 2 was filtered via a SpermPrep'@II column. The Percoll density gradient method was compared with the SpermPrep'@II method in a similar protocol using 43 ejaculates. Sperm populations recovered via the SpermPrep'@II filtration method showed significantly higher hypoosmotic swelling test results, acrosin profiles, and percentage of hyperactivated spermatozoa than sperm fractions recovered by the swim-up method. Furthermore, significant differences were found in most of sperm morphometric parameters between the above sperm populations. However, sperm fractions recovered via the SpermPrep'@II method did not show significantly different values for these same tests and for most of sperm morphometric parameters compared to the Percoll density gradient method. These results suggest that the SpermPrep'@II filtration and Percoll density gradient method are equally efficient in isolating sperm subpopulations with better functional parameters than the swimup method.