The metabolism of methylseleninic acid, MeSeA in the gastro-intestinal tract was studied by incubation of MeSeA with homogenized intestinal epithelial cells from pigs. The major selenium-containing metabolite was identified by analysis of the supernatant of the incubated cells by LC-ICP-MS. The identity of the compound was established by LC-ESI-MS/MS after purification by preparative chromatography. The metabolite appeared to be a selenium-sulfur amino acid, S-(methylseleno)cysteine (CH3Se–S–CH2CH(NH2)COOH). The selenium-sulfur ratio was confirmed to be 1:1 by simultaneous monitoring of selenium and sulfur as the oxides by LC-ICP-MS. Analysis of a synthesized standard of S-(methylseleno)cysteine by LC-ESI-MS resulted in the same mass spectrum with the same fragmentation pattern as the isolated metabolite. The formation of this selenium compound did not require enzymatic systems but only the presence of cysteine. The presence of this selenium compound in mammalian cell models after addition of MeSeA has not previously been reported.