We aimed to investigate inter-year variability in mating system and paternity in an experimental Norway spruce (Picea abies (L.) Karst.) clonal seed orchard that was established with five geographically distinct populations. Using five nuclear microsatellite markers, we analysed 1396 progeny of five mother trees representing each of the populations in three successive mast-years. Selfing varied among mother trees, ranging from 0% to 18.3% with a mean of 13.9% in 1994, 10.1% in 2004, and 7.6% in 2006. Considerable background pollination was observed in each of the three studied mast-years and reached ca. 58%. The paternity assignment conducted showed an uneven male contribution to the seed crop, what was partly related to the number of ramets per paternal clone. All provenances contributed to the seed crop, but with different input, and two provenances dominated. Effective pollen dispersal was significantly determined by distance, with 72.2% of the seed crop resulting from crosses at a distance of up to 15 m. Our study indicated that despite considerable differences in the geographic origin of populations, inter-mating between clones from each population was possible, which generally agrees with the expectations related to the establishment of this seed orchard.