Micro-channel chips, which are used in micro total analysis systems, are attracting attention in the medical field. The photolithography technology used in semiconductor manufacturing is generally used to manufacture micro-channel chip dies. However, this technology requires many processes, such as mask fabrication and the application of photoresist to a substrate, as well as expensive clean room facilities. Therefore, this study examines how to form a fine groove by cutting with micro-endmills. This report experimentally examined the cutting performance of the tool run-out. In addition, effects of the tool run-out on the micro-grove milling, such as decrease in the cutting force changing,and the tool wear, were clarified.