The accumulation of isoflavonoids has been associated with a incompatible response of soybean roots to infection by the root-knot nematode. Soybean isoflavonoids have been proposed to have many effects on host-pathogen interactions. The phytoalexin accumulated in soybean tissues in response to nematode infection is glyceollin, which is derived from the isoflavonoid precursor daidzein. Accumulation of the isoflavonoids genistin and daidzin and their aglycones genistein and daidzein in soybean roots following inoculation with Meloidogyne incognita race 3 was determined in the whole root system by high performance liquid chromatography (HPLC). The roots were harvested from controls and nematode-inoculated seedlings 1, 3, and 10 days after inoculation. Extractions were made from roots with ethanol and the extracts were analyzed for isoflavonoids by HPLC. There was no significant difference between susceptible cultivar Pickett 71 and the resistant cultivar FT-Cometa one day after inoculation for all isoflavonoids. Daidzein and genistein were detected for all evaluated cultivars inoculated and non-inoculated. The resistant cultivar FT-Cometa showed a higher concentration of daidzein than the Pickett 71 cultivar ten days after inoculation, which ranged from 0.181/100g of root at the first day after inoculation to 1.025 mg/100g of root at tem days after inoculation.