Pipecolic acid, a metabolite of lysine, is found in human physiological fluids. It is known that plasma pipecolic acid levels are elevated in patients with Zellweger syndrome, a genetic disorder, and chronic liver diseases. However, it is uncertain if this acid originates directly from food intake or from mammalian or intestinal bacterial enzyme metabolism. To characterize the relationship between plasma pipecolic acid and diet, we analyzed the contents of pipecolic acid in 17 edible plants and changes in plasma and urinary pipecolic acid levels following soybean juice ingestion by 4 healthy volunteers. Our study revealed that some of the plants contained high concentrations of total pipecolic acid, and a higher portion of L-isomer than D-isomer. Loading tests demonstrated that plasma levels and urinary excretion of D-isomer increased significantly 2 h after soybean juice ingestion. Plasma lysine levels showed a similar increase to that of D-isomer. These findings suggest that plasma pipecolic acid, particularly the D-isomer, originates mainly from the catabolism of dietary lysine by intestinal bacteria rather than by direct food intake and that D- and L-isomer may have different mechanisms of metabolism. Moreover, these findings may be important for clarifying the pathogenesis of peroxisomal disorders.