Bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most serious and economically important diseases of tomato worldwide, including Iran. Control of this disease is difficult due to seed-borne nature and long term survival of the bacterial agent on seed. A preventive disease management program based on using pathogen-free seeds and resistant cultivars is the best method for the disease control. In this research, effects of thermal treatment (44-64 ° C for 15, 25 and 35 minutes), chemical compounds (Bordeaux, Nordox, Copper oxychloride and Mancozeb at three different doses), and nine antibiotics (Nalidixic Acid, Gentamicin, Doxycycline, Streptomycin, Erythromycin, Cloxacillin, Rifampin, Cefalexin and Furazolidone) were investigated on tomato seeds disinfestation under laboratory conditions. The results showed that thermotherapy is a suitable approach for seed disinfestation as thermal treatment of 56 ° C for 35 minutes eliminated 98% of bacterial infestation without any effect on seed germination. In lower temperature, seed disinfestation was unsuccessful, and treatments of 60 and 64 ° C showed a significant negative effect on seed germination. Treatments with Rifampin, Nalidixic acid, Doxycycline and Gentamicin were effective in the elimination of 100% bacteria on seeds without any negative effect on seed germination. Treating infected seeds with the copper compounds showed that none of them were able to eliminate the bacteria, and significantly reduced seed germination. Overall, the application of the studied antibiotics is the most effective method for tomato seeds disinfestation for research purposes, but heat treatment at 56 ° C for 35 minutes for the practical application is recommended.