Single-cell measurements aid our understanding of chemically heterogeneous systems such as the brain. Lipids are one of the least studied chemical classes, and their cell-to-cell heterogeneity remains largely unexplored. We adapted microscopy-guided single-cell profiling using matrix-assisted laser desorption/ionization ion cyclotron resonance mass spectrometry to profile the lipid composition of over 30 000 individual rat cerebellar cells. We detected 520 lipid features, many of which were found in subsets of cells; Louvain clustering identified 101 distinct groups that can be correlated to neuronal and astrocytic classifications and lipid classes. Overall, the two most common lipids found were [PC(32:0)+H]+ and [PC(34:1)+H]+, which were present within 98.9 and 89.5% of cells, respectively; lipid signals present in <1% of cells were also detected, including [PC(34:1)+K]+ and [PG(40:2(OH))+Na]+. These results illustrate the vast lipid heterogeneity found within rodent cerebellar cells and hint at the distinct functional consequences of this heterogeneity.