The aim of this study was to validate a novel sperm purification device, the VetCount™ Harvester, for use in bovine in vitro fertilization (IVF). The device's performance was compared to BoviPure™ gradient centrifugation, a commercially available and accepted routine technique. Semen quality parameters were assessed for frozen-thawed semen from six different bulls (n = 6) following sperm purification. For each bull two semen subsamples were purified utilizing BoviPure™ gradient centrifugation and the VetCount™ Harvester, including a third subsample as untreated control. Both treatments significantly increased the proportion of progressively motile sperm cells (84.4 ± 14.1% and 85.1 ± 7.8%, respectively) compared to the untreated semen (41.9 ± 18.8%). BoviPure™ gradient and VetCount™ Harvester selected predominantly viable acrosome intact (VAI) sperm cells with low membrane fluidity and low free intracellular calcium concentration [Ca2+]i (76.5 ± 4.4% and 78.6 ± 6.0%). Normalizing [Ca2+]i of VAI sperm cells (non-treated semen: [Ca2+]i = 1) VetCount™ Harvester purified spermatozoa (0.67 ± 0.10) showed significantly lower [Ca2+]i than BoviPure™ treated sperm (0.84 ± 0.14; P < 0.05). Subsequently, the fertilizing ability of the spermatozoa was evaluated performing a competitive fertilization assay. Sperm cells from both treatment groups were fluorescently labelled using different dyes and added in equal amounts to in vitro matured oocytes. After 18 h co-incubation, the origin of the fertilizing sperm cell was evaluated via fluorescence microscopy. In two bulls, VetCount™ Harvester selected sperm that fertilized significantly more oocytes then BoviPure™ treated sperm, in another bull it was the opposite. For three bulls no difference was observed.We conclude that the VetCount™ Harvester selects a high-quality, fertile sperm fraction from frozen-thawed bull semen. However, some considerations have to be kept in mind for the direct use of the isolated sperm fraction in IVF.