Long chain alkenones and photosynthetic pigment derivatives (chlorins) are commonly employed biomarkers in the reconstruction of past sea surface temperatures (SSTs) and organic carbon export from the surface to the deep ocean. For these studies, marine sediment samples are often available which have been air dried or freeze-dried, given that these are common methods for removing water from sediments prior to microfossil analysis. We compared both drying procedures by analysing samples from two sediment cores (ODP 1087, southeast Atlantic and M36/2-MC435, North Atlantic). We found that significant losses of chlorins (>25%) and alkenones (up to 75%) occur with air-drying relative to freeze-drying. Changes in the composition of pigments are also likely. The alkenone unsaturation index U37K′ is sensitive to the drying method, showing an increase of up to 0.02 units relative to freeze-drying. However, this represents a maximum increase in SST estimates of only 0.5 °C. The tests suggest that freeze dried samples, rather than air dried sediments, should preferably be used to determine the sedimentary concentration of biomarkers. However, if chlorins are the main target compounds, wet extraction with acetone of sediment results in ca. 12% higher yield than the extraction of freeze-dried sediments with acetone/water. © 2007 Elsevier Ltd. All rights reserved.