A method for selenium speciation based on ion-chromatography (IC) microwave (MW) assisted on-line species conversion hydride generation (HG) atomic absorption spectrometry (AAS) is described. The conversion of selenium species into selenite was achieved by using hydrobromic acid and bromate. A potential interferent originating from the reagents was identified. Multivariate optimization of the IC-MW-HGAAS system was undertaken and the results show that the HBr/BrO₃⁻ ratio is a very important parameter, which should be carefully controlled both to obtain a high conversion efficiency and to diminish the interferent. The feasibility of the IC-MW-HGAAS system for real samples is demonstrated by the application of selenium speciation in extracts of the certified reference material CRM 402. The system is shown to be sensitive to interferences but the detection capability is good, relative detection limits being 1.0–1.6 ng g⁻¹ (based on a 50 μL injection volume) for the species investigated: selenomethionine, selenite, selenate and selenocystine. Selenate was quantified in the CRM 402 extract at a level of ≈1.5 μg g⁻¹ corresponding to ≈22% of the total selenium content in the material. The method described is concluded to be operationally defined because of the extraction procedure used.