The specificity, sensitivity, and versatility of mass spectrometry (MS) have made it the dominant analytical tool. However, typical biological and environmental samples are complex enough to require prior separations, especially to disentangle the ubiquitous isomers. The unique specificity of novel field asymmetric waveform ion mobility spectrometry (FAIMS) approach and its substantial orthogonality to MS make it attractive for isomer separations. The recently developed high-definition FAIMS enables previously impossible resolution of peptide and lipid isomers and even isotopomers. Here we broadly explore FAIMS separations of lipid isomers, focusing on the common glycerides and phospholipids. Analyses were performed using a custom planar FAIMS system coupled to the Thermo LTQ ion trap MS platform. We distinguished ~70% of isomers for protonated or ammoniated lipids generated by electrospray ionization, including all four major isomer types (stereo-numbering, chain-length, cis/trans, and double bond position). Further isomers were separated for metal-cationized (in particular, argentinated) lipids.