Generally, spermatozoa from most boars respond poorly to the challenge of cryopreservation, resulting in impaired survival. Post-thaw survivors often show unstable membranes, short life-span, and low fertilising capacity. As a result, the use of frozen-thawed boar spermatozoa for artificial insemination has not been wide-spread. The aim of the study was to improve post-thaw survival of boar spermatozoa by MACS. Membrane integrity, production of reactive oxygen species and mitochondrial membrane potential were measured in commercial semen doses obtained from Svenska Köttföretagen using flow cytometry. Spermatozoa from 36 semen doses were frozen as mini-flat-packs and stored in liquid nitrogen until analysis. After thawing, the spermatozoa were labelled with Annexin-V-coated magnetic particles and passed through a MACS column. The flow-through-fraction (FT), containing spermatozoa not exposing phosphatidylserine on their membranes, was collected. The properties of spermatozoa in FT and of those that were retained on the column were measured by flow cytometry, as well as the properties of frozen-thawed spermatozoa not passed through the column. Membrane integrity, which declined from a pre-freeze level of ≈80 % to ≈50% after thawing, was equivalent to pre-freeze levels after passage through the MACS column. For those spermatozoa retained in the column, the percentage of membrane intact spermatozoa was ≈25%. The ability to select membrane intact spermatozoa by MACS separation could result in improved quality in frozen-thawed boar semen samples and thus could be a step towards increasing the use of frozen-thawed boar semen for artificial insemination.