Time-of-flight secondary ion mass spectrometry (ToF-SIMS) can be utilized to map the distribution of various molecules on a surface with submicrometer resolution. Many of its biological applications have been in the study of membrane lipids, such as phospholipids and cholesterol. For these studies, the effectiveness of chemical mapping is limited by low signal intensity from various biomolecules. Because of the high-energy nature of the SIMS ionization process, many molecules are identified by detection of characteristic fragments. Cluster ion sources are able to increase ionization, leading to increased information collected from a surface. In this chapter, we highlight the utility of SIMS to image lipids at single cells. Particularly, we will describe sample preparation, data collection, and the analysis of lipids for two systems; rat oligodendrocytes and Tetrahymena thermophila. SIMS spectra yield information regarding lipid identity and concentration across cell surface.