A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this study, we used samples from 502 barn owls from continental and island populations across Europe, with the aim of quantifying and comparing the level of inbreeding between populations with differing demographic histories. In addition to comparing inbreeding status, we determined whether inbreeding is due to non-random mating or high co-ancestry within the population. We show that islands have higher levels of inbreeding than continental populations, and that this is mainly due to small effective population sizes rather than recent consanguineous mating. We assess the probability that a region is autozygous along the genome and show that this probability decreased as the number of genes present in that region increased. Finally, we looked for evidence of reduced selection efficiency and purging in island populations. Among island populations, we found an increase in numbers of both neutral and deleterious minor alleles, possibly as a result of drift and decreased selection efficiency but we found no evidence of purging.