Herein, we exploit the use of microfluidics and optimized Taylor cones for improved intrasource separation/selective ionization of lipid classes during electrospray ionization. Increased differential ionization of multiple phospholipid classes was achieved through microfluidics with chip‐based ionization resulting in substantial enhancement of intrasource separation/selective ionization of phospholipid classes in comparison to the conventional ion source. For example, using myocardial lipid extracts, 3‐fold improvements in intrasource separation/selective ionization of myocardial phospholipid classes were routinely realized in the negative‐ion mode in the absence of LiOH or other basic modifiers in the infused sample solutions. Importantly, the relative ratios of ions corresponding to individual molecular species in each lipid class to a selected internal standard from myocardial extracts were nearly identical between the chip‐based interface and the syringe‐pump‐driven capillary interface. Therefore, quantitation of individual lipid molecular species directly from biological extracts through comparisons with internal standards in each lipid class was readily accomplished with an accuracy and dynamic range nearly identical to those documented using the well‐established direct syringe‐pump‐driven capillary interface. Collectively, the use of microfluidics and robotic sample handling substantially enhances intrasource separation of lipids in comparison to routine capillary interfaces and greatly facilitates the use of multi‐dimensional mass spectrometry using shotgun lipidomics, thereby providing an automated and high‐throughput platform for global analyses of cellular lipidomes. Copyright © 2008 John Wiley & Sons, Ltd.