A chromatographic method for separating tear specific prealbumin (TSP) into six isoelectric forms is described. Size exclusion high performance liquid chromatography (SE-HPLC) was used to isolate TSP from whole tears, followed by chromatofocusing fast protein liquid chromatography (FPLC) of the SE-TSP fraction on a Mono P column. This yielded six fractions varying in isoelectric point (pI) between 5.3 and 4.6. Subsequent anion exchange FPLC (Mono Q column) allowed a slight further purification of each Mono P fraction and removed Polybuffer from the Mono P fractions. Isoelectric focusing (IEF) of the TSP isoforms verified that the heterogeneity was based on pI, and confirmed that the chromatofocusing separation was in many respects the same as an IEF separation. Purity of TSP isoforms was determined by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), IEF, enzyme-linked immunosorbent assay (ELISA) and immunoblotting of samples separated by SDS-PAGE and IEF. Amino acid analysis and N-terminal amino acid sequencing revealed subtle differences between the TSP isoforms. The entire purification procedure was conducted both with and without the addition of reducing agents and protease inhibitors to tear samples and all buffers used in the purification process. Relatively little difference was seen in the TSP isoform profile under these two sets of conditions. However, the tendency of isolated TSP to aggregate and precipitate was dramatically decreased under reducing conditions, resulting in significantly higher protein recoveries. This chromatographic purification procedure provides a basis for further study of the nature of the heterogeneity of TSP and characterization of the properties of this protein.