In order to analyze the structural features of small lignin fragments that are closely associated to polysaccharides, lignin carbohydrate complex (LCC) with low lignin content was extracted with water from the residual wood meal (sugi. Cryptomeria japonica) of milled wood lignin (MWL) isolation. This LCC exhibited almost the same neutral sugar composition as those extracted by other LCC solvents (dimethylformamide, dimethylsulfoxide, and others) but the lignin content was only 5.3%, which was much lower than others. Gel filtration chromatography demonstrated that lignin in this LCC was found together with carbohydrates at the higher molecular weight region, but after the treatment with carbohydrate-degrading enzymes the apparent molecular weight of both lignin and carbohydrates decreased significantly. Using a mild alkaline treatment, the apparent molecular weight of lignin also decreased while that of polysaccharide was not affected. These data indicated that lignin in this LCC is present as small fragments attached to high molecular weight polysaccharide at least partly by alkali-unstable linkages. Structural analysis by ozonation method revealed that the lignin in this LCC was lower in erythro/threo ratio of beta-O-4 structure and relatively richer in the threo type structure carrying C-aryl linkages at beta-position (beta-5 and/or beta-1) than other lignin fractions present in MWL, LCCs extracted by other solvents, and their extraction residues. It was suggested that the chemical structure of lignin closely associated to carbohydrates was different from that of the main part of lignin.