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There is consistent evidence that long-chain polyunsaturated fatty acids (LCPUFA) belonging to the <i>n</i>-3 series, i.e., eicosapentaenoic (20:5<i>n</i>-3, EPA) and docosahexaenoic (22:6<i>n</i>-3, DHA) acids, decrease the risk of heart, circulatory and inflammatory diseases. Furthermore, the bioavailability of such fatty acids has been shown to depend on their location in triacylglycerol (TG) molecules at the <i>sn</i>-2 position. Consequently, great attention has been accorded to the synthesis of structured acylglycerols (sAG), which include EPA or DHA at the <i>sn</i>-2 position. The aim of this work was to synthesize sAG starting from deodorized refined commercial salmon oil. For this, immobilized lipase B from <i>Candida antarctica</i> (nonspecific) was used as a catalyst for the intra–interesterification process under CO₂ supercritical conditions (CO₂SC). According to the CO₂SC reaction time, three different fractions including sAG compounds were obtained. The location of EPA and DHA at the <i>sn</i>-2 position in the resulting glycerol backbone was identified by mass spectrometry (MALDI-TOF) analysis. In all fractions obtained, a marked decrease in the starting TG content was observed, while an increase in the DHA content at the <i>sn</i>-2 position was detected. The fraction obtained after the longest reaction time period (2 h) led to the highest yield of <i>sn</i>-2 position DHA in the resulting sAG molecule.