A post-column isotope dilution analysis (IDA) methodology was applied to carry out quantitative speciation of selenium in human vitreous humor samples by size exclusion chromatography (SEC) coupled on-line to inductively coupled plasma mass spectrometry (ICP-MS). Two main selenium species detected by SEC-ICP-MS were found to be associated to protein complexes. The expected molecular weights for both selenium-bound complexes were confirmed by MALDI-TOF(MS) and the results matched well with the theoretical mass of a GPx monomer (M, 22 kDa) and tetramer (T, 88 kDa). The quantification of the two detected selenium-bound complexes by post-column IDA showed that the total content of selenospecies in vitreous humor was approximately 3.2 ± 1.8 ppb Se. Moreover, in most of the analyzed vitreous humor samples, the majority of the selenium was associated to higher molecular weight GPx biomolecules. In an attempt to assess if the enzymatic activity was associated with a given selenium-bound GPx protein, the antioxidant enzyme activity was assayed for the two separated GPx species. Only for GPx (T) was a linear relationship between activity and total Se concentration found by ICP-MS.