This study was conducted to develop a reliable method for control of set-borne inoculum of Verticillium and Fusarium species that cause the internal discoloration of horseradish roots. Horseradish propagative root stocks (sets), 0.5 to 3.0 cm in diameter and 20 to 25 cm long, were treated by immersing them into water at 44, 45, 46, 47, 48, 49, and 50 °C for 10, 20, and 30 min. Treated and untreated sets were cultured on acidified potato dextrose agar to determine the presence of the pathogens in the sets. Treatments at temperatures lower than 46 °C did not control the set-borne inoculum of the pathogens. Treated and untreated sets were also planted in the greenhouse and fields to assess the effects of the thermotherapy on germination of the sets and vigor of the plants. Treatments at 48 °C or greater either delayed or reduced set germination and reduced plant vigor. The most effective treatment for control of the set-borne pathogens without adverse effects on set germination or plant vigor was determined to be 47 °C for 20 min.