The effects of organic solvents on the capillary electrophoresis (CE) separation of a number of important biological porphyrin methyl esters - six weakly basic, hydrophobic cyclic tetrapyrroles possessing two and four to eight methyl ester groups around the periphery of the porphyrin ring - were investigated in the mode of micellar electrokinetic chromatography (MEKC), microemulsion electrokinetic chromatography (MEEKC), and nonaqueous CE. In aqueous MEKC, partial separation of the six neutral porphyrin methyl esters was obtained with an organic modifier (acetonitrile) in the concentration range between 20 and 40%, in which sodium dodecyl sulfate (SDS) molecules might be present in the form of SDS micelles and/or SDS micelle-like aggregates. Relatively stable SDS micelles can be formed in nonaqueous MEKC using formamide as the separation medium, but the separation of the target analytes remained unsatisfactory. Improved resolution of all six porphyrin methyl esters was obtained using MEEKC with the running buffer consisting of 0.8% w/w n-heptane (oil phase), 2.25% w/w SDS and 1.0% w/w Brij 35 (mixed surfactant), 6.6% w/w 1-butanol (cosurfactant), and 30% v/v 2-propanol (second cosurfactant), but reproducibility in terms of peak areas for certain porphyrins (especially uroporphyrin I octamethyl ester) was found to be very poor. Best separation performances were achieved with nonaqueous CE separations in which the weakly basic porphyrin methyl esters were protonated under strongly acidic conditions (e.g., using 10 mM perchloric acid) in mixed organic solvents. For example, using a 50:50 mixture of methanol and acetonitrile as the separation medium, baseline separation of all six (positively charged) porphyrin methyl esters can be obtained within 3 min and the average precision (RSD, N = 13) in terms of migration time and peak area were 0.55 and 2.16%, respectively.