A combination of reversed-phase high-performance liquid chromatography (RP-HPCL) and capillary zone electrophoresis (CZE) was used for the characterization of peptide maps of swine pepsin after its digestion with alpha-chymotrypsin. Peptide maps obtained by both methods were compared and five selected chromatographic peaks were identified on an electrophoreogram. The different order of peaks found in RP-HPLC compared to CZE confirmed the complementarity of these two methods. More peptide fragments were resolved by RP-HPLC, which was also found to be less sensitive to salt content in peptide mixtures, than by CZE, but only CZE was able to separate and identify phosphorylated and dephosphorylated peptide fragments of swine pepsin digest. CZE provides faster separation than RP-HPLC, however, the salts have to be removed by ultrafiltration or by RP-HPLC pre-separation prior to CZE analysis. Combined use of RP-HPLC and CZE for peptide mapping makes it possible to distinguish between the phosphorylated and dephosphorylated forms of swine pepsin. This is important from a diagnostic point of view, because pepsin phosphorylation may be associated with gastric cancer.