Trace and ultra-trace levels of selenium are routinely determined in many laboratories using hydride generation–quartz furnace atomic absorption spectrometry. However, as more is understood about the role of selenium in toxicity and dietary studies, there is an increasing need to provide species-specific information from complex biological and environmental samples. As the hydride generation process requires the selenium to be in the selenium(IV) oxidation state, prior reduction of any selenium(VI) present in the sample is necessary. This step is conventionally accomplished by maintaining the sample at an elevated temperature in the presence of hydrochloric acid, although this approach suffers from a number of disadvantages, including the loss of information on the original selenium species present in the sample. This paper describes an on-line system for the determination of inorganic selenium species in which the sample is first analysed for selenium(IV), and then microwave energy is then used to reduce selenium(VI) and provide a total selenium measurement. As full control of the microwave reduction step is possible, the approach lends itself to a totally automated selenium speciation system. Detection limits and precision are unaffected by the on-line reduction step.