Although semen cryopreservation has been applied successfully in a few species, considerable variation in post-thaw semen viability exists. Independent of sperm quality before freezing, the semen of certain individuals will consistently freeze badly, resulting in poor motility, disrupted acrosome and plasma membrane, and thus reduced fertilising ability, indicating the existence of variation in membrane properties within species. A more comprehensive understanding of sperm cryobiology would be obtained by the investigation of within-species variation in the susceptibility of spermatozoa to cryoinjury. This review aims to explore the phenomenon of consistent variation in frozen semen quality between species and between individuals in an effort to find new insights into the reasons for cryoinjury. Recent studies suggest that there is a genetic basis for variation in post-thaw semen quality, and argue that modern molecular technologies are able to identify markers linked to genes influencing this variation. The identification of genetic differences between individuals, which may be linked to cryosurvival, provides an opportunity to develop a functional and molecular understanding of the factors that influence semen cryopreservation, allowing selective breeding of desired traits and the development of genetic tests that predict the outcome of semen freezing.