During gas chromatography (GC) analysis of fatty acid (FA) composition of the dinoflagellate Gymnodinium kowalevskii, we found unex-pectedly low and irreproducible content of all-cis-3,6,9,12,15-octadecapentaenoic acid (18:5n-3), which is an important chemotaxonomic marker of several classes of microalgae. We compared chromatographic behavior of 18:5n-3 methyl ester and other GC derivatives obtained using different conventional methods of derivatization. The use of methods based on saponification or base-catalyzed transesterification resulted in a mixture of double-bond positional isomers of 18:5. On a SUPELCOWAX 10 column, the equivalent chain length (ECL) value for authentic 18:5n-3 methyl ester was 20.22, whereas the main component after base-catalyzed methylation had ECL 20.88. Attempts to prepare N-acyl pyrrolidides or 4,4-dimethyloxazoline (DMOX) derivatives of 18:5n-3 also gave inadequate results. These derivatives also showed a main peak corresponding to isomerized 18:5. Mass spectra for both DMOX and pyrrolidide derivatives of this compound showed the base peak at m/z 139, probably corresponding to 2,6,9,12,15-18:5 acid. Of all methods tested for methylation, only derivatization with 5% HCl or 1% sulphuric acid in methanol gave satisfactory results. Therefore, GC or GC-mass spectrometry analyses of algal lipids containing 18:5n-3 may be inaccurate when base-catalyzed methods of FA derivatization are applied. The best and simplest way to avoid incorrect GC results is to use standard acid-catalyzed methylation.