An investigation of the basic factors which govern the microemulsion electrokinetic chromatography (MEEKC) and micellar electrokinetic chromatography (MEKC) separation of Hematoporphyrin D and its base hydrolysis product, hematoporphyrin derivative (HpD), was performed. These model compounds contain a complex mixture of porphyrin monomers, dimers and/or oligomers, and were utilized to gain insights into the MEEKC/micellar electrokinetic chromatography (MEKC) separation of samples containing highly lipophilic substances. For example, the organic modifier/cosurfactant (1-butanol) and/or oil phase (e.g., 1-octanol in comparison to ethyl acetate) were found to have an apparent influence on the separation selectivity of Hematoporphyrin D, the extent of which was dependent on the chemical nature of the surfactant employed (e.g., sodium dodecyl sulfate vs. sodium cholate). An interesting and important finding was that the presence of an organic modifier (methanol or acetonitrile at a concentration of 20% or higher) in the sample matrix as well as in the run buffer was essential for the optimal MEEKC or MEKC separation of a number of porphyrin monomers (including hematoporphyrin IX and its acetates, most likely hydroxyacetate, diacetate, and vinyl acetate, as well as its dehydration products, hydroxyethylvinyldeuteroporphyrin and protoporphyrin) contained in Hematoporphyrin D. On the other hand, the use of these optimized conditions for the MEEKC or MEKC separation of various oligomeric porphyrin species in HpD were unsatisfactory. As HpD is a well-known and effective photosensitizing agent in photodynamic therapy (a new approach for cancer treatment), the improved separation and characterization of various monomeric and oligomeric porphyrin species in HpD and its starting material, such as Hematoporphyrin D, is a challenging and important task.