An unidentified o-phthaldialdehyde positive substance is often present at significant concentrations in extracts of intracellular amino acids from diatoms, dinoflagellates and prymnesiophytes. This compound elutes in reverse phase HPLC protocols similar to that of Lindroth & Mopper (1979; Analyt. Chem. 51: 1667-1674), near or with glutamine or histidine and may thus result in errors of quantification of those amino acids. As a consequence, errors in the estimation of the Gln/Glu ratio, an index of C-N status in algae, are possible. In addition there are other compounds, some present at significant levels (notably a compound in prymnesiophytes), which elute near or with other protein amino acids. A modification to the HPLC protocol is described which not only results in the elution of the major compounds away from any of the other common 20 amino acids, but which also gives a better separation of glycine and threonine which formally were often resolved poorly.