We report analysis of both inorganic and amino acid forms of selenium by ion chromatography with inductively coupled plasma atomic emission spectroscopic detection. Three chromatographic systems are compared; effects of representative sample matrices on the separations are investigated. We are unable to resolve selenate and seleno-cystine using the Dionex AS4A column. Elution of seleno-cystine and seleno-cysteine is strongly suppressed in samples of bacterial cell extract matrix analyzed with the Dionex AS10 column; this interference is not observed with the Dionex AS11 column. Synthetic sea water sample matrix has little effect on analytical results. Quantitation parameters are reported.