Selection medium is important in sperm isolation for assisted reproductive technologies. Contrary to the naturally occurring human cervical mucus which has a high viscosity, most current practices for motility based sperm selection use a low viscosity medium. In this study, we used a microfluidic device to assess the effects of high viscosity media made with hyaluronic acid (HA) and methyl cellulose (MC) on bovine and human sperm motility and viability (sperm transferred directly from cryoprotectant). The microfluidic penetration test, viability, and motility were compared for sperm swimming in both HA and MC media with about 20cp viscosity (measured at 20°C). Our resulted indicate that MC medium resulted in a significantly higher number of viable bovine sperm penetrating the medium as compared to HA. Furthermore, MC resulted in the selection of a sperm subpopulation with a 274% increase in sperm viability in comparison to the raw semen, while HA increased viability by only 133%. In addition to viability, bovine sperm motility parameters were significantly higher in the MC medium as compared with HA. Experiments with human sperm swimming in MC indicate that sperm swim slower and straighter at higher viscosities. In conclusion, the results indicate that in a micro-confined environment representative of the in vivo environment, MC is a preferred high viscosity medium to ensure the highest concentration of motile and viable sperm.