This paper presents an initial approach towards polyether ether ketone (PEEK) microfluidic structures for chemical analysis by introducing PEEK capillary electrophoresis (CE) chips. PEEK shows outstanding material features, such as extremely high chemical resistance and mechanical stability, high temperature resistance, very low adsorption. However, difficulties in PEEK processing have limited its application until now. Here, a new plasma enhanced thermal bonding process is introduced and resulting features of the microstructures are investigated.