We analyzed speleothem calcite from the Oregon Caves National Monument, southwestern Oregon, to determine the preservation, distribution, concentrations and sources of aliphatic lipid compounds preserved in the calcite. Maximum speleothem growth rate occurs during interglaciations and minimum during glacial intervals. Concentrations of the total lipid compounds range from 0.5 to 12.9 μg g−1. They increase at times of low speleothem growth rate, suggesting dilution, whereas the apparent accumulation rate of lipid compounds tends to be highest during times of fastest speleothem growth rate. Such increased accumulation generally corresponds to times of warm (interglacial) climate, suggesting either a greater source of organic materials during interglacial times and/or greater efficiency of compound capture during more rapid calcite growth. Aliphatic lipid compounds include homologous n-alkanoic acids, n-alkanols and methyl n-alkanoates and sterols with concentrations ranging from 0.3 to 7.8 μg g−1, 0.4 to 1.1 μg g−1, 0.5 to 9.6 μg g−1 and 0.1 to 2.7 μg g−1, respectively. Minor amounts of branched methyl n-alkanoates and dimethyl n-alkanedioates are also present. The high concentrations of methyl n-alkanoates are the result of esterification reactions of free fatty acids in alkaline solutions with high pH values associated with the dripping cave waters. The distribution patterns and geochemical parameters and indices indicate that the major sources of the aliphatic lipids involved leaching from higher plants and microbial residues derived from the soil zone above the cave system. The estimated percentage of microbial inputs ranged from 42 to 90% of the total lipids and also showed an increase in accumulation during warm climates. These well-preserved lipid compounds in speleothem calcite could be used as biomarkers for paleoenvironmental study.