In a novel approach to the use of macrocycles in separation systems, we report the use of macrocyclic ligands as electroosmotic flow modifiers for the separation of inorganic anions by capillary electrophoresis (CE). Inorganic anions were successfully separated through the use of 18-crown-6 or cryptand 2.2.2. as electroosmotic flow modifiers. We found that for our CE system, use of a macrocycle as the modifier resulted in better baseline stability and better efficiency than the commonly used modifier DETA. In our system, the separation efficiency and electroosmotic flow varied according to the pH of the buffer and the affinity of the macrocycle for the buffer metal cation. Results for sodium- and potassium-based buffers show that for the cryptand, pH plays a role in determining the amount of macrocycle-metal complex formed. Separations of a 12 anion standard illustrate these results. In addition, we report the effect of concentration of both macrocycle and metal ion on complex formation and resultant electroosmotic flow modification. Relationships between the macrocycle-metal complex, the buffer medium, the efficiency of separation, and the migration times of the analytes are discussed, and theoretical interpretations presented.