Polycyclic Aromatic Sulfur Heterocycles (PASHs) are undesirable compounds in fuels and refined petroleum-based products. Capillary electrophoresis (CE) was investigated as an alternative to analyze the preisolated PASHs from partially desulfirized materials derived from Athabasca, Canada, bitumen. The sample complexity is considerably reduced by this preisolation by ligand exchange chromatography on a Pd(II) containing phase and subsequent ionization of the neutral PASHs through S-methylation to impart electrophoretic mobility. The PASH components are separated and characterized using CE with a time-of-flight mass spectrometer (TOF MS) as detector. An additional major advantage of the CE separation is that the drawbacks of HPLC (limited separation efficiency) and GC (volatility limitations) for separations of high molecular weight compounds can be circumvented. CE was demonstrated to be a highly efficient method in the separation of PASHs and up to 200,000 theoretical plates were obtained. The practicability of the method was shown by an extensive qualitative analysis of the PASH fraction of a hydrotreated middle distillate and a hydrotreated heavy gas oil. Additional information on the sample composition like the identity of parent ring systems, the alkyl substitution, and hydrogenated products from the hydrodesulfurization was gained through the use of CE-TOP MS and measuring standard PASHs expected to be present. The results are compared with GC-MS and high-resolution Orbitrap measurements of the same samples.