Compound specific hydrogen isotopic compositions (δD) of free and bound forms of n-fatty acids (FA) were measured throughout a 200 m sediment core taken from Lake Biwa to assess application of biomarker δD values to paleoclimate study in this central Japan lake. The results of our study suggest that the sources of the C16 n-FA in the two forms are different, whereas both free and bound C28 n-FA originate from terrestrial plants. The δD of combined (free plus bound) C28 n-FA in the 200 m sediment core shows a large variability, with relatively low and high values during the glacial and interglacial periods, respectively. Based on comparison of our record with other marine and lacustrine paleoclimate data, we found that the sedimentary record of C28 n-FA δD likely reflects the temperature-induced change in δD of summer precipitation. This finding suggests that δD values of C28 n-FA could be used as a proxy for summer paleotemperatures in the sediments of Lake Biwa and other lakes. Copyright © 2012 John Wiley & Sons, Ltd.