Mesopelagic fish collected during 3 field campaigns in 2020 were analysed for their lipid content. The sampling was conducted on 5 main locations; 2 stations in the Western Mediterranean Sea (September/October), 4 stations in the North Atlantic off the Iberian Peninsula (October), 4 stations in the Irminger Sea (July), 5 stations in the Iceland Basin (July) and 4 stations in the Northern Norwegian Sea (May). The fish were collected at distinct depth intervals, with different trawl types depending on the vessel. The database consists of 28 mesopelagic fish species belonging to 9 families and 5 genera. For each record, length and wet weight of the fish analysed is recorded with the wax ester (WE), triacylglycerol (TAG) and phospholipid (PL) values as % of total lipids (TL). Each data record is associated with information on the sampling location, geographic coordinates, month and year of sample collection, sampling gear and depth, taxonomic ranks (phylum, class, order, family), and number and replicates analysed. The lipids were extracted following Folch's extraction method (Folch et al. 1957), which was implemented on whole fish or a weighted sub-sample of a homogenized whole fish. Individual lipid classes were separated by Thin Layer Chromatography (TLC). A lipid sample was spotted onto silica-coated quartz rods, (chromarods; SES GmbH) and the lipid classes separated by development in two solvent systems: hexane/diethyl ether/acetic acid (60:17:0.2, by volume) followed by hexane/diethyl ether (96:4 vol/vol). The analysis was performed using an Iatroscan MK 5 TLC-FID analyser.