Intramyocellular lipids are of importance in lipid-related diseases. The techniques in this field are limited because of a lack of adequate tools for localization of various lipids. The most usual methods for the localization of lipid distribution in the skeletal muscle are histochemistry and fluorescence probes. Different chromatography methods and mass spectrometry techniques have also been used for lipid identification. Our aim was to localize the spatial distribution of lipids in their native forms by using static time-of-flight secondary-ion mass spectrometry (TOF-SIMS). Human percutaneous skeletal muscle biopsies were obtained from the middle part of the lateral vastus muscle in the right leg of healthy adolescents with a body mass index >30. Samples were prepared by high-pressure freezing, freeze-fracturing and freeze-drying, and analysed by imaging TOF-SIMS equipped with a Bi3+ cluster ion gun. In the positive spectra, we identified phosphocholine, cholesterol, diacylglycerol, phospholipids and triacylglycerol. Phosphocholine was localized to the edge of the fibre, representing the sarcoplasma or endomysium. Weak cholesterol signals were observed in the intracellular areas. High diacylglycerol and low triacylglycerol signal intensities were seen in intracellular spaces of the transversal area of the muscle fibre. In the negative spectra, we identified fatty acids. We observed co-localization of fatty acids and diacylglycerol, which may indicate lipid-storing parts of the skeletal muscle. Thus, TOF-SIMS imaging can be used to depict the heterogeneous localization of lipids in human skeletal muscle.