Organic acids are essential flavor components in alcoholic beverages such as wine and sake (Japanese rice wine). The effects of fumarase deficiency on the productivity of malic, fumaric and succinic acids in Saccharomyces cerevisiae were examined using the FUM1 gene disruptant. The single nuclear gene FUM1 encoding fumarase in S. cerevisiae, DBY746, was disrupted by a site-directed one-step gene disruption technique. The fumarase activity of the isolated FUM1 disruptant was abolished. The FUM1 disruptant having a pet phenotype showed no growth on minimal medium containing glycerol as a carbon source even after prolonged incubation. The productions of organic acids by the FUM1 disruptant in YPD liquid culture containing 10% glucose and in sake mash were analyzed by HPLC. The analytical results of the FUM1 disruptant showed there were no differences in extracellular malate productivity, fumarate productivity had increased, and that succinate productivity was reduced compared with those of the control strain. In the production of sake using the FUM1 disruptant, fermentation ability as monitored by CO2 evolution was not different from that of the control strain. These results indicate that site-directed FUM1 disruption alters organic acid production without any loss of fermentation ability in yeast.