Metabolite profile is a powerful analytical technique to identify the functional characterization of plants. In this study, the phytochemicals and secondary metabolites of lentils (Lens culinaris) were analyzed to compare the anti-oxidative activities according to the different colors. The polar metabolites, fatty acids, carotenoids, flavonoids, anthocyanins, total phenolic acids, DPPH activity were analyzed. Three kind of lentils, French green whole lentil (FG), red whole lentil (LR), and green whole lentil (LG) (ASIA SEED Co., LTD), were used for this study. Fatty acids, phytochemicals, and antioxidative components from each lentil varieties were analyzed by official methods. The contents of lutein in carotenoids were 6-9 times higher than zeaxanthin in all lentils, but were not significantly different among three varieties. The content of carotenoids in FG was lower significantly than those in the LR and LG. Myricetin and luteolin were detected in the only FG. Kaempferol and delphinidin were significantly highest in the FG. Most of the phenolic acids except coumarate were higher in FG and LG than in LR. Also antioxidant effects (EC50) were higher in FG and LG than in LR. The analyzed metabolites obtained from lentils showed distinct separation in the PCA results according to the varieties. Also, lentils showed different anti-oxidant profiles according to the colors. FG and LG showing higher contents of phytochemicals showed higher antioxidative activity than LG containing relative low contents of phytochemicals.