To establish the use of low-pressure carbon dioxide microbubbles (MB-CO2), developed as a food sterilizing method, as a practical technique for inactivating plant pathogens in hydroponic nutrient solution, Fusarium oxysporum f. sp. melonis and Pectobacterium carotovorum subsp. carotovorum were inactivated by MB-CO2. The inorganic components in the MB-CO2-treated hydroponic nutrient solution were also analyzed, and a growth test of leaf lettuces with the MB-CO2-treated hydroponic nutrient solution was performed. Five-log reductions in F. oxysporum f. sp. melonis spores and P. carotovorum subsp. carotovorum cells were achieved by MB-CO2 treatment performed at 15°C and 1.5MPa in the mixing vessel, and at 40°C or 45°C and 4.0MPa at the heating coil. No changes of the inorganic components in the MB-CO2-treated hydroponic nutrient solution were observed. Furthermore, CO2 dissolved in the hydroponic nutrient solution at high concentration by MB-CO2 treatment had little influence on the growth of leaf lettuces. MB-CO2 appears to be a promising new technique for inactivating plant pathogens in hydroponic nutrient solution. © 2013 Elsevier B.V.