When whole cells are subjected to pyrolysis gas chromatography/mass spectrometry (Py-GC/MS) analysis, it provides biochemical profiles containing overlapping signals of the majority of compounds. To determine marker compounds that discriminate embryogenic calluses from nonembryogenic calluses, samples of embryogenic and nonembryogenic calluses of five higher plant species were subjected to Py-GC/MS. Genetic programming of Py-GC/MS data was able to discriminate embryogenic calluses from nonembryogenic calluses. The content ratio of 5-meyhyl-2-furancarboxaldehyde and 5-(hydroxymethyl)-2-furancarboxaldehyde was greater in nonembryogenic calluses than in embryogenic calluses. However, the content ratio of phenol, p-cresol, and $^1H-indole$ in embryogenic calluses was 1.2 to 2.4 times greater than the ratio in nonembryogenic calluses. These pyrolysates seem to be derived from the components of the cell walls, which suggests that differences in cell wall components or changes in the architecture of the cell wall playa crucial role in determining the embryogenic competence of calluses.