Intracellular lipid pools are highly dynamic and tissue-specific. Physical exercise is a strong physiologic modulator of lipid metabolism, but most studies focus on changes induced by long-term training. To assess the acute effects of endurance exercise, mice were subjected to one hour of treadmill running, and 13 C 16 -palmitate was applied to trace fatty acid incorporation in soleus and gastrocnemius muscle and liver. The amounts of carnitine, FFA, lysophospholipids and diacylglycerol and the post-exercise increase in acetylcarnitine were pronouncedly higher in soleus than in gastrocnemius. In the liver, exercise increased the content of lysophospholipids, plasmalogens and carnitine as well as transcript levels of the carnitine transporter.13 C 16 -palmitate was detectable in several lipid and acylcarnitine species, with pronounced levels of tracer-derived palmitoylcarnitine in both muscles and a strikingly high incorporation into triacylglycerol and phosphatidylcholine in the liver. These data illustrate the high lipid storing activity of the liver immediately after exercise whereas in muscle, fatty acids are directed towards oxidation. The observed muscle-specific differences accentuate the need for singlemuscle analyses as well as careful consideration of the particular muscle employed when studying lipid metabolism in mice. In addition, our results reveal that lysophospholipids and plasmalogens, potential lipid signalling molecules, are acutely regulated by physical exercise.Certain lipids such as ceramides, diacylglycerols, and acylcarnitines have been shown to activate intracellular signalling cascades and to regulate metabolic pathways [1][2][3][4] . Intracellular accumulation of these lipids in liver and skeletal muscle is frequently related to a chronic inflammatory state and to the development of metabolic diseases 5,6 . However, lipid bioactivity per se is a physiological event and it is only the deregulated production and storage of lipids that leads to a non-physiological activation of signalling pathways 7 . Physical exercise induces tissue-specific alterations in substrate supply and utilization that are evident as increased turnover of fatty acids 8 and elevated levels of acylcarnitines 9 . Previous studies addressed the hepatic lipid response to long-term training 10 or the exercise-dependent regulation of the intramyocellular triglyceride pools in skeletal muscle 11 , but the acute regulation of other lipid species by one bout of exercise is less well understood. Thus, changes in the levels of individual lipid signaling molecules could play a role in the acute response to physiological challenges that affect lipid metabolism.While it is reasonable to expect differences in the regulation of lipid species between organs such as liver and muscle, less attention is usually paid to the distinct metabolism of individual skeletal muscles. Muscles contain different myofibres with specific metabolic and contractile properties. The main classification for different types of muscle fibres is into "slow"...