The microsomal epoxide hydrolase (mEH) plays a significant role in the metabolism of numerous xenobiotics. Additionally, it has a potential role in sexual development and bile acid transport, and it is associated with a number of diseases, such as emphysema, spontaneous abortion, eclampsia and several forms of cancer. Toward developing chemical tools to study mEH biological role, we designed and synthesized a series of absorbent and fluorescent substrates. The highest activity for both rat and human mEH was obtained with the fluorescent substrate cyano(6-methoxy-naphthalen-2-yl)methyl glycidyl carbonate (11). An in vitro inhibition assay using this substrate ranked a series of known inhibitors similarly to the assay that used radioactive cis-stilbene oxide, but with a greater discrimination between inhibitors. These results demonstrate that the new fluorescence-based assay is a useful tool for the discovery of structure-activity relationships among mEH inhibitors. Further, this substrate could also be used for the screening chemical library with high accuracy and with a Z' value about 0.7. This new assay permits a significant decrease in labor and cost as well as offering the advantage of a continuous readout. However, it should not be used with crude enzyme preparations due to interfering reactions.