Fagopyrum esculentum (Buckwheat) is a globally used alternative crop that contains several useful substances with various effects; however, many of these substances (rutin, quercetin, etc.) are water insoluble. To extract these substances, alcohols is required, which is inconvenient because these solvents cause diverse problems. Many studies are underway to achieve effective extraction of these substances with water. Among of these studies, microwave assisted water extraction (MAE) has been performed extensively. In this study, we performed the extraction in various solvents and/or microwave from Fagopyrum esculentum. The analysis of the content of useful substances and the bioactivity were performed and shown to increase in MAE. Liquid chromatography-mass was performed in order to identify of the useful water-insoluble substances. Catechin, quercetin, and rutin, which are all insoluble in water, were hardly extracted with water even on heating (4.4 ppb, 3.9 ppb and 60.3 ppb, respectively). However, MAE was found to extract much more of these substances than water (1204 ppb, 110.8 ppb and 2946 ppb, respectively). Although less efficient than alcohols, MAE showed much higher efficiency than simple water extraction. These results indicate that water extraction using microwave technology is effective in cases where it is difficult to extract useful substances using water.