Offspring quality may benefit from genetic dissimilarity between parents. However, genetic dissimilarity may trade-off with additive genetic benefits. We hypothesized that when sexual selection produces sex-specific selective scenarios, the relative benefits of additive genetic vs. dissimilarity may differ for sons and daughters. Here we study a sample of 666 red deer (Cervus elaphus) microsatellite genotypes, including males, females and their foetuses, from 20 wild populations in Spain (the main analyses are based on 241 different foetuses and 190 mother-foetus pairs). We found that parental lineages were more dissimilar in daughters than in sons. On average, every mother was less related to her mate than to the sample of fathers in the population when producing daughters not sons. Male foetuses conceived early in the rutting season were much more inbred than any other foetuses. These differences maintained through gestation length, ruling out intrauterine mortality as a cause for the results, and indicating that the potential mechanism producing the association between parents’ dissimilarity and offspring sex should operate close to mating or conception time. Our findings highlight the relevance of considering the sex of offspring when studying genetic similarity between parents.