Microwave techniques are widely used in acid digestion of solid samples. Their use in the extraction of organic analytes from environmental samples is less widespread, despite commercial devices being available for this purpose and the potential for reducing analysis time and solvent consumption. We report the use of microwave-assisted extraction (MAE) of biomarkers (chlorins and long-chain C37 alkenones), which are used as palaeoclimatic proxies in marine sediments. Factorial design was applied to determine the influence of temperature, volume of solvent and extraction time on the efficiency of the extraction of total chlorins. We found that only changes in temperature produced significant variation in yield. The extraction temperature of MAE was then optimised for both chlorins and alkenones. Equivalent results to repeated extractions by ultrasonication were obtained from a single extraction step of 5 min using 10 ml of solvent at a temperature of 70°C. MAE was found to be a more efficient, faster and less labour-intensive method than ultrasonic extraction. Assessment of the influence of extraction conditions for MAE on the relative recovery of alkenones showed that this technique is a feasible option in the measurement of U37K′ in marine sediments. © 2003 Elsevier Ltd. All rights reserved.