Stability of soybean isoflavone isomers according to extraction conditions such as temperature, pH, and extracting solvents was investigated. Heating induced three chemical reactions to occur for malony1 derivatives of isoflavones, namely decarboxylation of malony1 groups into acety1 derivatives, deesterification of malony1 residues, and hydrolysis of $eta$-glycosidic bonds. Among the twelve isoflavone isomers, change in concentrations of acety1glycosides were most pronounced: Acety1 derivatives were present only in trace amounts in unheated hypocotyls, but the content increased dramatically during heating. As for the glycosides, concentrations of daidzin and glycitin increased due to heat treatment, though that of genistin remained almost unchanged. Heat decomposition rates and the patterns differed among the three malony1 derivatives. After 120 min at $80^{circ}C$, the relative concentrations of daidzin, glycitin and genistin were increased from $9.2\%$, $12.4\%$ and $3.3\%$ to $19.3\%$, $21.9\%$ and $6.2\%$, respectively. When crude isoflavones were solubilized in glycine buffer (pH 10.0) and incubated at $80^{circ}C$, deesterification occurred faster than at pH 7.0. When the pH of isoflavone solution was increased, the malony1glycosides were hydrolyzed to their respective glycosides at increased rate. Both acetyl and aglycone forms were unchanged and only de-esterification reactions occurred. At the acidic pH, malonylglycosides were much stable both at 60 and $80^{circ}C$. However at pH 10, $80^{circ}C$ and 1 hr, $75-80\%$ of malonylglycosides were transformed to their deesterified glycosides. When isoflavones were extracted with $60\%$ aqueous ethanol at $60^{circ}C$, isoflavone isomers were stable and the deesterification reactions did not occur in these conditions. However, at $80^{circ}C$ deesterification of malonyiglycosides occurred significantly with $15-20\%$ of malonylglycosides being hydrolyzed into their respective glycosides. This experiment showed that malonylglycosides undergo decomposition when heated or exposed to alkaline conditions. Also, aqueous ethanol was preferred to aqueous methanol as solubilizing media for obtaining extract with minimum degradation of malonylglycosides.