Chlorinated fatty acid methyl esters, transesterified from the lipids of eel (Anguilla anguilla, obtained from the receiving waters of a chlorine bleaching pulp mill), were studied by gas chromatography (GC) using electrolytic conductivity detection and mass spectrometry (MS) with electron impact and ammonia positive-ion chemical ionization. GC retention indices and column difference values in combination with GC/MS demonstrated the presence of isomers of methyl dichlorotetradecenoate, methyl dichlorohexadecenoate, methyl dichlorooctadecenoate and methyl tetrachlorotetradecanoate. Isomers of methyl threo, threo-tetrachlorooctadecanoate were identified by co-injection of the eel sample and synthesized reference compounds. The results were confirmed by ammonia positive-ion chemical ionization high-resolution selective-ion monitoring of the ammonium adduct molecular ions.