The ca. 13 m long sediment core PG1351, recovered in 1998 from the central part of Lake El’gygytgyn, NE Siberia, was investigated for lithostratigraphy, water content, dry bulk density (DBD), total organic carbon (TOC), total nitrogen (TN), total sulphur (TS) and biogenic silica (opal) contents, and for TOC stable isotope ratios (δ13CTOC). The event stratigraphy recorded in major differences in sediment composition match variations in regional summer insolation, thus confirming a new age model for this core, which suggests that it spans the last 250 ka BP. Four depositional units of contrasting lithological and biogeochemical composition have been distinguished, reflecting past environmental conditions associated with relatively warm, peak warm, cold and dry, and cold but more moist climate modes. A relatively warm climate, resulting in complete summer melt of the lake ice cover and seasonal mixing of the water column, prevailed during the Holocene and Marine Isotope Stages (MIS) 3, 5.1, 5.3, 6.1, 6.3, 6.5, 7.1–7.3, 7.5, 8.1 and 8.3. MIS 5.5 (Eemian) was characterized by significantly enhanced aquatic primary production and organic matter supply from the catchment, indicating peak warm conditions. During MIS 2, 5.2, 5.4, 6.2 and 6.4 the climate was cold and dry, leading to perennial lake ice cover, little regional snowfall, and a stagnant water body. A cold but more moist climate during MIS 4, 6.6, 7.4, 8.2 and 8.4 is thought to have produced more snow cover on␣the perennial ice, strongly reducing light penetration and biogenic primary production in␣the lake. While the cold–warm pattern during␣the past three glacial–interglacial cycles is probably controlled by changes in regional summer insolation, differences in the intensity of the warm phases and in the degree of aridity (changing snowfall) during cold phases likely were due to changes in atmospheric circulation patterns.