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A simple liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) method for determination of the eicosapentaenoic acid (EPA) concentration to arachidonic acid (AA) concentration ratio in human saliva has been developed. The EPA/AA ratio in serum or plasma is widely recognized as a useful indicator in identifying the risk of cardiovascular disease, especially atherosclerosis. The salivary EPA/AA ratio is expected to be a convenient alternative to the serum or plasma EPA/AA ratio, because saliva offers the advantages of easy and noninvasive sampling. The saliva was deproteinized with acetonitrile, purified using an Oasis HLB cartridge, and derivatized with 1-[(4-dimethylaminophenyl)carbonyl]piperazine (DAPPZ). The derivatized EPA and AA were subjected to LC/ESI-MS/MS, and the EPA/AA ratio was determined using the selected reaction monitoring mode. The DAPPZ-derivatization increased the ESI sensitivity by 100- and 300-fold for EPA and AA, respectively, and enabled the detection of trace fatty acids in saliva using a 200L sample. The assay reproducibility was satisfactory (relative standard deviation, <5.0%). The method was successfully applied to the measurement of the salivary EPA/AA ratios of healthy Japanese subjects and their changes owing to the supplementation of EPA. Copyright (c) 2015 John Wiley & Sons, Ltd.