Lipid biomaker compounds (n-alkanoic acids, n-alkanols, sterols, n-alkanes, chlorophyll derivatives) and total lipid carbon in a chloroform extractable fraction, isolated from sedimentary deposits up to approximately 2 Ma old of a 1400 m core sample of Lake Biwa, were analyzed by gas chromatography, gas chromatography-mass spectrometry and a thin-layer chromatography-flame ionization detection analyzer (TLC-FID) to investigate their diagenesis and their utilities as biomakers. The samples are divided into two parts at a depth of 911.4 m. The samples below 911.4 m are basement rock. The upper core is composed of clay from the surface to 249.5 m in depth, and alternated with slit, clay and gravels from 249.5 to 911.4 m. The organic compound carbon, obtained by hydrolysis of the lipid fraction by alkali solution, comprised from 11 to 35% of the total lipid carbon. TLC-FID analysis indicated that significant amounts (about 70-80%) of the total lipid carbon were present in the polar fraction and small proportions were simple lipids. The amounts of n-alkanols were comparable to those of n-alkanoic acids and sterols, while contemporary lacustrine sediments usually contain a larger amount of n-alkanoic acids than of n-alkanols. Normal alkanes, maximizing in abundance at C27 or C29, were most abundant among the lipid compounds. Variation in the distributions of sterols and stanols seemed to preserve the information of input sources and the C27/C29 ratios were correlated to the C/N of the sediments. The composition of n-alkanols, maximizing at C24 or C18, appeared to indicate an aquatic paleoenvironment-a paleowater depth at least in the upper 250 m. Ratios of shorter to longer chain n-alkanoic acids, which had been believed to be an indicator of autochthonous to allochthonous origins, clearly increased with time. A marked correlation between chlorophyll derivatives (ratio of chlorophyll derivatives to total lipid carbon) and paleotemperature was found.