The detailed studies concerning capillary electrophoresis separation of aminophosphonic acid enantiomers with various commercially available cyclodextrins are presented. The obtained results show that the separation of these stereoisomers is dependent on pH of background electrolyte, concentration of cyclodextrin as well as on the type of applied chiral selector. The separation mechanism is based on the co-operative effect of hydrogen bond type interactions enhanced by hydrophobic forces and sterical constrains between aminophosphonate and cyclodextrin. With application of elaborated method, enantiomeric baseline or partial separation of 18 alpha-aminophosphonic acids was achieved. This separation can be successfully used for routine aminophosphonic acids enantiopurity determination.