In this study a flow injection (FI) system used in conjunction with hydride generation (HG), atomic absorption spectrometry (AAS) and microwave (MW) aided pre-reduction of selenite (Se(IV)) to selenate (Se(IV)) with HCl:HBr has been developed in order to differentiate both inorganic selenium species. As full control of the MW reduction step is possible, the experimental approach allows the use of milder acidic conditions (10% v/v of HCl and HBr) than those conventionally accomplished with hydrochloric acid alone (>/=50% v/v). Experimental parameters were optimized by the univariate optimization method. In either case, the linear range was from 1.0 to 30 mug l(-1). The detection limits based on 3sigma of the blank signal were 0.25 mug l(-1) for Se(IV) and 0.30 mug l(-1) for Se(VI). The reproducibility, about 3% RSD and recoveries of different amounts of Se(VI) and Se(IV) added to water and orange juice samples (97-103%) were good. The main advantage of the proposed method is that the sequential determination of Se(IV) and Se(VI) is performed at a high sampling frequency (ca. 50 samples per h) in a closed system without Se losses, and with a minimum sample waste, operator attention, and sample manipulation.