A vesicle mediated high performance liquid chromatographic (HPLC)–microwave digestion (MW)–hydride generation (HG) system coupled on-line with atomic absorption spectrometry (AAS) and inductively coupled plasma mass spectrometry (ICP-MS) has been assessed for selenium species separation and detection. Selenocystine, selenomethionine, selenoethionine, selenourea, Se^IV and Se^VI are separated by vesicle mediated chromatography prior to on-line selenocompounds microwave digestion with a KBrO₃–HBr mixture to generate Se^IV continuously, which is finally transformed into SeH₂, in a continuous manner with a merging flow of sodium tetrahydroborate(III). Analytical characteristics of this coupling are compared with those obtained coupling HPLC–ICP-MS via conventional nebulisation. Detection limits (DLs) obtained for selenocystine, selenomethionine, selenoethionine, selenite and selenate in spiked human urine, when ICP-MS was used as detector, ranged between 1.0 and 5.3 µg l^–1 (51–267 pg), while precision ranged between±3.4 and±8.4%. This continuous system, vesicle mediated HPLC–MW–HG–atomic detection, allows the separation and detection of selenocystine, selenourea, selenomethionine, selenoethionine, selenite and selenate in human urine. The analytical versatility of such coupling (with ICP-MS as the atomic detector) allows basal selenium speciation in urine. Three different normally occurring selenium species in human urine, simply diluted (1+1), have been found. The relative sophistication of the vesicle mediated–HPLC–MW–HG–ICP-MS interface, versus HPLC–ICP-MS via conventional nebulisation, can be justified because of its considerably higher sensitivity for most of the selenocompounds assayed, lower matrix interferences and the possibility of simultaneous interference free ⁷⁷Se and ⁷⁸Se monitoring.