AbstractA miniature mechanical seal with cooling water circulating system has been developed as a shaft seal for rotary blood pumps. The present paper describes the establishment of the experimental methods under blood sealing and the estimation of the effect of the surface roughness on the shaft seal problems, especially in the increase of the friction and the leakage. Micro‐leakage rates of the blood and the cooling water were measured by an ion chromatography. In this method, the ion concentration was converted into the leakage rate. The frictional loss torque was measured by a torque meter. Results are provided with three types of surface roughness, Ra = 0.009 µm, Ra = 0.088 µm and Ra = 0.170 µm. It is shown that as the surface roughness increases the leakage decreases while the frictional loss torque increases under blood sealing. The best surface roughness in the torque and the leakage characteristics were different. Copyright © 2010 John Wiley & Sons, Ltd.