The G2 form of butyrylcholinesterase (BChE) of mucosal cells of rat intestine is a rare amphiphilic species, which is related to class II of acetylcholinesterase. Preliminary work indicated that the enzyme can bind heparin and suggested particular properties as compared to other BChEs. Ionic properties of the G2 form BChE were studied with different ionic exchangers. Heparin-Sepharose chromatography, nondenaturing electrophoresis and sucrose gradient centrifugation were used to study heparin interaction with the G2 form BChE. The enzyme structure was modified with reagents that react specifically with amino groups (p-hydroxyphenylglyoxal and 2,4,6-trinitrobenzene sulfonic acid). The G2 form was not retained by DEAE-cellulose which was generally used to isolate BChE from human serum, but was completely bound by strong cation exchanger (Dowex 50). Heparin-Sepharose quantitatively retained the enzyme which was partially eluted only by charged compounds. Nondenaturing gel electrophoresis showed a reduction in enzyme migration with increasing concentrations of heparin and chondroitin sulfate, but not with heparan sulfate. Triton X-100 dissociated the G2 form into monomers but failed to reverse the association between the enzyme and heparin. Reagents specific to amino groups indicated that arginine and lysine residues were involved in this association. In summary, these studies demonstrate that the ionic properties of the G2 form BChE are involved in the binding with heparin. Our results rule out the possibility of amphiphilic interactions in the formation of heparin-enzyme complex and indicate that amino groups are predominately involved in this association.