The application of metal-sensitive and -specific detection systems could essentially increase the information content of the results from high-resolution separation systems used for the determination of different metal-containing species (e.g. in medicine, ecology, biochemistry). Many separations are performed in capillaries or miniaturized systems (GC, CE, microbore HPLC) which possess very low detection volumes in the nanolitre region. For the generation of detectable X-ray signals from the analytes inside the capillary PIXE (proton-induced X-ray emission) was used after the pretreatment of the capillaries by laser ablation or with etching solutions. The coupling is demonstrated by signals achieved for a pressure-driven capillary systems as well as for CE using capillaries with 75–100 μm I.D. The influence of capillary pretreatment and the design of the PIXE measuring chamber on the signals is demonstrated. With the introduced experimental setup the limits of detection have been 10 −5, M or less for various metals, e.g. As, Cu, Fe, Ni, Pb, Rb, Y and Zn. An comparison with direct and indirect UV detection modes is performed and examples for the speciation of arsenic and lead compounds are discussed as well as potentialities for the improvement of the technique and the decrease of the limit of detection of the analytes.