Horseradish (Armoracia rusticana, Brassicaceae) is a crop that seldom produces viable seed and is propagated exclusively via vegetative (or clonal) procedures for commercial production. Male sterility and self‐incompatibility (SI) have been suspected as possible mechanisms underlying sterility in horseradish. Therefore, greenhouse and laboratory analyses were conducted to assess pollen viability, pollen recognition in pistils, and to quantify success in self‐ and cross‐pollination events using various horseradish clones. Pollen viability was high (98–100%); consequently, male sterility was an unlikely explanation for low seed set. Self‐pollination in some horseradish clones produced seed, although most clones showed some level of SI. Significant numbers of pollen tubes were found in ovaries of self‐compatible (SC) individuals soon after stigmas were saturated with pollen; furthermore, between three and six ovules with pollen tubes were found in the micropyle which correlates with the number of seed typically found in mature fruits from outcrossed or SC individuals. The results of this study suggest variation in the breeding system of horseradish, as some clones exhibit complete SC, while other clones are SI that recognize and reject self‐pollen.