<i>Background:</i> Pipecolic acid, a metabolite of lysine, is found in human physiological fluids and is thought to play an important role in the central inhibitory γ-aminobutyric acid system. However, it is unclear whether plasma <i>D</i>- and <i>L</i>-pipecolic acid originate from oral food intake or intestinal bacterial metabolites. <i>Methods:</i> We analyzed the contents of <i>D</i>- and <i>L</i>-pipecolic acid in several processed foods including dairy products (cow’s milk, cheese and yogurt), fermented beverages (beer and wine) and heated samples (beef, bovine liver, bread and tofu) to clarify the relationship between plasma <i>D</i>- and <i>L</i>-pipecolic acid and dietary foods. <i>Results:</i> Our study revealed that some of the samples contained high concentrations of total pipecolic acid, and a higher proportion of <i>L</i>- than <i>D</i>-isomers. The other samples also showed high proportions of <i>L</i>-pipecolic acid. It was also shown that there is no significant change in the ratio of the <i>D</i>-isomer before and after heat treatment. The heat treatments could not cause the racemization of pipecolic acid in this study. <i>Conclusion:</i> These findings suggest that plasma pipecolic acid, particularly the <i>D</i>-isomer, does not originate from direct food intake and that <i>D</i>- and <i>L</i>-pipecolic acid can possibly be derived from intestinal bacterial metabolites.