A time-based flow injection (FI) separation system coupled to electrothermal atomic absorption spectroscopy (ETAAS) has been developed for the determination of selenium in parenteral solutions. Selenate interacts with L-methionine, which is immobilized on controlled pore glass (CPG), at pH 3.0 and eluted with HCl (10% v/v). Total selenium content is determined directly by ETAAS without preconcentration and selenite is calculated by difference. The features of the separation system are: 100% efficiency of retention and an enhancement factor of 20 for a pre-concentration time of 6 s (sample flow rate = 10 mL min^-1) with HCl elution volumes of 50 µL. The detection limit (3σ) was 6 ng L^-1, and the relative standard deviation (n = 10) at the 0.1 µg L^-1 level is 3.0%. The method has high selectivity and was applied to the determination of Se (IV) and (VI) in parenteral solutions with satisfactory results.