By studying the geochemistry of amino acids, we attempt to clarify uncertainties in the radiocarbon chronology and in correlations of ash beds and pollen spectra in lacustrine sediment from Clear Lake, California. Two amino acids, aspartic acid and alanine, are considered in detail. Relative concentrations of aspartic acid decrease with depth, a result likely due to diagenesis and to preferential adsorption and hydrolysis in clay. Relative concentrations of alanine show the reverse effect with depth, probably due, in part, to the generation of alanine from other amino acids during diagenesis. The aspartic acid racemization rate calibrated by radiocarbon yields anomalously low age and temperature estimations for Clear Lake when kinetic assumptions from a study in Lake Ontario are used. However, the “apparent” alanine racemization rate correlates well with the alanine racemization rate determined for sediments from Lake Biwa, Japan. Our age assessment based on alanine supports a time-depth curve obtained from oak pollen and oxygen isotopes for Clear Lake representing a time span of about 130,000 yr.