Oxygen plasma treatment has been used extensively to bond polydimethyl siloxane to polydimethyl siloxane or glass in the rapid prototyping of microfluidic devices. This study aimed to improve the bonding quality of polydimethyl siloxane to passivated silicon using oxygen plasma treatment, and also to evaluate the bonding quality. Four types of passivated silicon were used: phosphosilicate glass, undoped silicate glass, silicon nitride and thermally grown silicon dioxide. Bonding strength was evaluated qualitatively and quantitatively using manual peel and mechanical shear tests respectively. Through peel tests we found that the lowering of plasma pressure from 500 to 30 mTorr and using a plasma power between 20 to 60 W helped to improve the bond quality for the first three types of passivation. Detailed analysis and discussion were conducted to explain the discrepancy between the bonding strength results and peeling results. Our results suggested that polydimethyl siloxane can be effectively bonded to passivated silicon, just as to polydimethyl siloxane or glass. © 2006 IOP Publishing Ltd.