Reconstruction of paleodiets for hunter-gatherers in Japan is carried out using the major nutritive elements. (1) Carbohydrate sources are examined using carbon isotope data from charcoal in burnt “cookies” and pottery residues. Measurements of charcoal in burnt cookies indicated no evidence of C4 plant use during the prehistoric age in Japan. (2) Protein sources are identified using carbon and nitrogen isotope ratios measured on collagen extracted from human bones. Among hunting-fishing-gathering people in Japan, marine protein intake was about 70-90% for people in Hokkaido including the Ainu people, while Jomon people in Honshu and Kyushu had a wider variation of 20-60% between coastal and inland people. (3) Lipid sources are identified from fatty acids and sterols extracted from pottery residues and coprolites by GC and GC-MS. Coprolites and pottery sherds from shellmidden sites indicated that animal foods were dominant lipid sources in the diet, and marine food resources were not constantly, but occaisionally used.