Thermally unaltered conodont elements, brachiopods, and vertebrates were analyzed with reverse phase high profile liquid chromatography to locate and quantify amino acid remnants of the original organic matrix in the fossils. No consistent similarities in amino acid content were found in conodont taxa, and criteria based on organic residues appear to have no taxonomic significance in the fossils tested from these localities. However, hydroxyproline, an amino acid that is found in the collagen molecules of animals, as well as in the glycoproteins in the cell walls and reproductive tissues of certain plants, is represented in most taxa. The organic matter retained in the impermeable crowns of conodont elements might have been derived originally from a form of collagen. Biochemical analyses, correlated with histochemical tests, demonstrate that organic matter is an integral part of the hyaline tissue of the element crown and not the result of surface contamination. Tests of a range of vertebrate and invertebrate fossil hard tissues produced similar results. The analyses indicate that hyaline tissue in the conodont element crown is not a form of vertebrate enamel, which contains no collagen. Albid tissue, with little or no organic content, is not a form of vertebrate bone or dentine, both based on collagen and low in mineral. Although these results do not help to determine the phylogenetic affinities of conodont animals, they indicate that conodont elements do not contain hard tissues characteristic of vertebrate animals.