Structured lipids (SL) were synthesized by the interesterification reaction between medium-chain triacylglycerols and eicosapentaenoic acid (EPA) ethyl ester. The products were partially purified, and the fatty acid at the sn-2 position was determined after pancreatic lipase-catalyzed hydrolysis. The effect of additives (water and glycerol) on the rate of reaction was also investigated. Mol% EPA incorporated into the triacylglycerols was increased by adding water when trilaurin and tricaprylin were the substrates and IM 60 was the biocatalyst, With SP 435, EPA incorporation was always less with additional water than without water. The addition of glycerol (0.005 g or 0.01 g) improved interesterification catalyzed by IM 60 to some degree, but an excess amount (0.02 g) inhibited the reaction. The reaction with glycerol showed no significant difference with SP 435. After scale-up and fractionation by column chromatography, we could recover approximately 0.3-0.4 g of product/g of reaction products. After hydrolysis by pancreatic lipase, we can conclude that IM 60 has a high specificity for sn-1,3 positions. With SP 435 lipase, 34.8-39.3 mol% of EPA was found at the sn-2 position of the recovered SL.