Pathogenic strains of the soilborne fungus Periconia circinata produce peritoxins with host-selective toxicity against susceptible genotypes of sorghum. The peritoxins are low-molecular-weight, hybrid molecules consisting of a peptide and a chlorinated polyketide. Culture fluids from pathogenic, toxin-producing (Tox⁺) and nonpathogenic, non-toxin-producing (Tox) strains were analyzed directly by gradient high-performance liquid chromatography (HPLC) with photodiode array detection and HPLC-mass spectrometry to detect intermediates and final products of the biosynthetic pathway. This approach allowed us to compare the metabolite profiles of Tox⁺ and Tox strains. Peritoxins A and B and the biologically inactive intermediates, N-3-(E-pentenyl)-glutaroyl-aspartate, circinatin, and 7-chlorocircinatin, were detected only in culture fluids of the Tox⁺ strains. The latter two compounds were produced consistently by Tox⁺ strains regardless of the amount of peritoxins produced under various culture conditions. In summary, none of the known peritoxin-related metabolites were detected in Tox strains, which suggests that these strains may lack one or more functional genes required for peritoxin biosynthesis.