Although secondary ion mass spectrometry (SIMS) has been successfully employed for mapping lipid distributions at the cellular level, the identification of intact lipid species in situ is often complicated by isobaric interference. The high mass resolution and tandem MS capabilities of a C60-QSTAR hybrid instrument has been utilized to identify over 50 lipid species from mouse macrophages (RAW 264.7). In this investigation, lipid assignments made based on mass accuracy were confirmed with tandem MS analyses. Data obtained from C60-SIMS was compared to liquid chromatography (LC)-MS data obtained by the LIPID MAPS consortium. A majority of the lipids detected with LC-MS, but not detected with C60-SIMS, were present at concentrations below 2.0 pmol/µg of DNA. Matrix-related effects prevented the detection of lipids with the glycerophosphoethanolamine (PE) headgroup, glycerophosphoserine (PS) headgroup and lipids with polyunsaturated fatty acyl chains in the C60-SIMS analyses. Lipid distributions obtained from a lawn of RAW 264.7 cells stimulated with the endotoxin KDO2-Lipid A were also studied. The results obtained with C60-SIMS agreed with the established LC-MS data for the glycerophosphoinositol lipid class (PI) with adequate molecular sensitivity achieved with as few as 500 cells. Copyright © 2012 John Wiley & Sons, Ltd.