The beneficial effects of n-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on depression are not definitively known. In a previous population-based prospective cohort study, we found a reverse J-shaped association of intake of fish and docosapentaenoic acid (DPA), the intermediate metabolite of EPA and DHA, with major depressive disorder (MDD). To examine the association further in a cross-sectional manner, in the present study we analyzed the level of plasma phospholipid n-3 PUFAs and the risk of MDD in 1,213 participants aged 64-86 years (mean 72.9 years) who completed questionnaires and underwent medical check-ups, a mental health examination, and blood collection. In multivariate logistic regression analysis, odds ratios and 95% confidence intervals were calculated for MDD according to plasma phospholipid n-3 PUFA quartiles. MDD was diagnosed in 103 individuals. There were no significant differences in any n-3 PUFAs (i.e., EPA, DHA, or DPA) between individuals with and without MDD. Multivariate logistic regression analysis showed no significant association between any individual n-3 PUFAs and MDD risk. Overall, based on the results of this cross-sectional study, there appears to be no association of plasma phospholipid n-3 PUFAs with MDD risk in the elderly Japanese population.