A new approach to assess the orthogonality of two-dimensional (2-D) separation systems based on conditional entropy is developed. It considers the quantitative distribution of peaks in the entire separation space such that the orthogonality obtained is independent of the number of peaks observed for each separation technique. Therefore, it can be used to compare the orthogonality of different 2-D separation protocols for a given sample. Herein, the developed method has been employed to estimate the orthogonality of peptide separation by off-gel electrophoresis (OGE) hyphenated to capillary zone electrophoresis (CZE).