The TEX86 ratio has been proposed as a palaeotemperature proxy for reconstructing surface water temperatures in aquatic environments. It is based on measuring the relative abundance of membrane lipids of marine Crenarchaeota, namely glycerol dialkyl glycerol tetraethers (GDGTs). Here we describe the rapid screening of GDGTs in sediments and water particulate matter with an optimized method using HPLC coupled to an ion trap mass spectrometer. The reproducibility of the analysis is as good as 0.012 (RSD 2.2%) for TEX86, thus providing a reproducible method for GDGT analysis. Preliminary results are shown for sediments from small as well as large lakes and for sediment trap material from Lake Baikal. GDGTs are present in most of the samples and TEX86 values are presented along with estimated temperatures. © 2006 Elsevier Ltd. All rights reserved.