Analytical HPLC is a compounds separation tool that have better performances. The ability of the separation was not able to separate isomered saponins with physicochemical properties are very similar. It has been found two isomered saponins of an amorphous crystalline pure seed Kolowe (C. excelsus). The saponin separation using preparative HPLC column, and the results of analytical HPLC analytical column against the amorphous crystal showed a peak which indicates that it is a pure crystalline amorphous. However, the results of spectroscopic analysis with NMR-2D in a variety of techniques, the pure amorphous crystal is two saponins isomered. Two saponin are 3-O-[b-D-Xylopyranocyl(1®3)-b-D-glucopyranocyl(1®2)-b-D-glucuronopyranocyloxy]–28-O-(2- methylbuthyroyloxy)-oleana-12-en-15a, 16a, 22a-trihydroxy and 3-O-[b-D-Xylopyranocyl (1®3)-b-Dglucopyranocyl( 1®2)-b-D-glucuronopyranocyloxy]-28-O-(3-methylbuthyroyloxy)-oleana-12-en-15a, 16a, 22a- trihydroxy.