Individuals can avoid inbreeding or competition with kin via long-distance natal dispersal. On the other hand, staying close to the well-known natal area may be a safer choice with respect to recruiting opportunities, reproductive success and the individual's survival probability as well. Natal dispersal strategy often differs between sexes, being generally female-biased in birds. We explored if the Carpathian Basin White-tailed Eagle population shows fine scale genetic structure and if it does, what is the extent of philopatry in the two sexes. We furthermore investigated sex bias in natal dispersal distance inferred from spatial distributions of genetically close relative breeding females and males. Spatial autocorrelation analyses failed to find fine-scale genetic structure, despite the species being known to be philopatric. Pairwise breeding distances of close relatives showed female bias according to Wilcoxon rank sum test. The median distance of two close relative females was 136 km, while it was only 38 km in males. Since White-tailed Eagles are known to be faithful to their breeding territory, we assumed that the breeding distance between an individual and its parents refers to the individual's natal dispersal distance. Due to the same reason, the breeding distance of two siblings should also be related to their individual dispersal distances from their shared natal area. Therefore, we argue that the difference we found between sexes in pairwise breeding distances of close relatives stands for a female-biased natal dispersal. This bias may be a consequence of the species' breeding strategy, and it decreases the inbreeding probability as well.