Soybean fermented by Bacillus subtilis natto is called NATTO, which is one of Japanese traditional foods. Processing of NATTO needs long immersion time for water impregnation into dried soybeans. In this study, the effect of high hydrostatic pressure (HHP) on the processing of whole and crushed soybeans was investigated. Soybean samples were first of all immersed in water and then treated with HHP of up to 200 MPa. Water content of whole soybean was increased by 3% and 5% with pretreatment at 45°C for 60min and successive treatments at 50 MPa and 200 MPa, respectively. Compared with conventional NATTOs, the amount of amino acids in whole NATTO decreased but that in crushed NATTO increased by approximately 2 times. Total amount of isoflavons in both NATTOs was not significantly influenced by HHP treatment.