An improved HPLC method is presented, which allows separation and quantification of a broad range of lipid classes of marine zooplankton with special regard to neutral lipids. Marine zooplankton species often produce high amounts of exceptional lipids, especially at high latitudes, in order to cope with the harsh environmental conditions and strong seasonality in food supply. Major neutral lipid classes are wax esters, triacylglycerols, diacylglycerol ethers, free fatty alcohols and sterols. Neutral and polar lipids were separated and identified on a monolithic silica column (Chromolith®Performance-Si) using high performance liquid chromatography (HPLC) with an evaporative light scattering detector (ELSD). The method resolves a broad spectrum of lipids, varying in polarity from squalene to lysophosphatidylcholine in a single run. The total run time was 35 min including column re-equilibration. The calibration was made at levels of 0.1-60 μg lipid/injection, but a 10-15-fold greater amount can be injected if single lipid classes need to be separated, e.g. for further determination of individual fatty acids. The method was applied to representative Arctic zooplankton species (copepods, pteropods, euphausiids and ctenophores) that are known to biosynthesize in particular neutral lipids like diacylglycerol ethers and free fatty alcohols. © 2009 Elsevier B.V. All rights reserved.