The effect of the positional distribution of docosahexaenoic acid (DHA) within triacylglycerol (TAG) molecules on the oxidative stability of oil-in-water emulsions was investigated by using a synthetic TAG regio-isomer pair SDS (1,3-dioctadecanoyl-2-[4,7,10,13,16,19-docosahexaenoyl] glycerol) and SSD (1,2–dioctadecanoyl-3-[4,7,10,13,16,19-docosahexaenoyl] glycerol), where S and D represent stearic acid and DHA, respectively. Oil-in-water emulsions (10%, w/w) of each isomer were subjected to accelerated autoxidation by continuous exposure to air at 50C in the absence of light. Oxidation during the exposure (storage) was monitored by measuring a series of volatile compounds characteristic of DHA oxidation. SSD emulsion oxidized faster than SDS emulsion, showing that DHA is more stable to oxidation when located at the sn-2 position of the TAG compared with the sn-1(3) position. This regio-isomeric effect is similar to that previously reported for bulk oil oxidation.