Organic matter preserved in speleothems has considerable potential to record changes in the surrounding environment, particularly in the overlying vegetation. Here, we review three types of organic matter analysis relevant to speleothems: organic fluorescence, lipid biomarker analysis, and amino acid racemisation. Organic matter luminescence provides a useful non-destructive and rapid method for assessing dissolved organic matter quantity and quality, while biomarker analysis (amino acids and lipids) has the potential to provide a more detailed signal related to specific parts of the surrounding ecosystem such as the dominant vegetation regime and bacterial activity. Amino acid analysis has yet to prove demonstrably useful in stalagmites, due to the inability to characterise the sources of proteinaceous matter. However, the small but increasing body of work on lipid biomarker analysis in stalagmites has shown that a wide variety of recognisable biomarkers are preserved over long periods of time (>100 ka), can be recovered at temporal resolutions of <10 yr, and show meaningful changes through time. This approach is therefore of considerable potential value to Quaternary science. © 2008 Elsevier Ltd. All rights reserved.