Addition of long-chain polyunsaturated fatty acids (LC-PUFAs) from marine oil into food products implies preliminary refining procedures of the oil which thermal process affects the integrity of LC-PUFAs. Deodorization, the major step involving high temperatures, is a common process used for the refining of edible fats and oils. The present study evaluates the effect of deodorization temperature on the formation of LC-PUFA geometrical isomers. Chemically isomerized eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were used as reference samples. Fish oil samples have been deodorized at 180, 220 and 250 °C for 3 h and pure EPA and DHA fatty acid methyl esters (FAMEs) were chemically isomerized using p-toluenesulfinic acid as catalyst. FAMEs prepared from fish oil were fractionated by reversed-phase high-performance liquid chromatography (RP-HPLC). Geometrical isomers produced by both processes were fractionated by silver-ion thin-layer chromatography (Ag-TLC) and silver-ion high-performance liquid chromatography (Ag-HPLC). The FAME fractions were subsequently analyzed by gas chromatography (GC) on a 100 m highly polar cyanopropylpolysiloxane coated capillary column, CP-Sil 88. Our results show that thermally induced geometrical isomerization appears to be a directed reaction and some ethylenic double bond positions on the hydrocarbon chain are more prone to stereomutation. Only minor changes were observed in the EPA and DHA trans isomers content and distribution after deodorization at 180 °C. The analyses of EPA and DHA isomer fractions revealed that it is possible to quantify EPA geometrical isomers by GC using the described conditions. However, we notice that a mono-trans isomer of DHA, formed during both chemical and thermal treatments, co-elute with all-cis DHA. This feature should be taken into consideration for the quantification of DHA geometrical isomers.