Genetic methods enable to reveal cryptic parental contributions in reproduction, especially in socially monogamous species. The rate of extra-pair paternity is generally low in raptors and owls and its presence in some species is tightly associated with sequential polyandry which can rarely occur in years with high food availability. In this study we investigated the mating system of the Tengmalm's owl (Aegolius funereus) in the Ore Mountains (Czech Republic). In this area, the species usually nests in high breeding densities which could increase an opportunity for extra-pair copulations. In total, 297 individuals (54 females, 47 males and 196 juveniles) from 46 nest boxes were genotyped at seven microsatellite loci. We present results of a five-year study and four extra-pair nestlings (2.3 %) were detected which did not result from sequential polyandry.