The authentication of the physico-chemical properties of ginsenosides reference materials as well as qualitative and quantitative batch analytical data based on validated analytical procedures is a prerequisite for certifying good manufacturing practice (GMP). Ginsenoside Rb1 and Rg1, representing protopanaxadiol and protopanaxatriol ginsenosides, respectively, are accepted as marker substances in quality control standards worldwide. However, the current analytical methods for these two compounds recommended by Korean, Chinese, European, and Japanese pharmacopoeia do not apply to red ginseng preparations, particularly the extract, because of the relatively low content of the two agents in red ginseng compared to white ginseng. In manufacturing fresh ginseng into red ginseng products, ginseng roots are exposed to a high temperature for many hours, and the naturally occurring ginsenoside Rb1 and Rg1 are converted to artifact ginsenosides such as Rg3, Rg5, Rh1, and Rh2 during the heating process. The analysis of ginsenosides in commercially available ginseng products in Korea led us to propose the inclusion of the (20S)- and (20R)-ginsenoside Rg3, including ginsenoside Rb1 and Rg1, as additional reference materials for ginseng preparations. (20S)- and (20R)-ginsenoside Rg3 were isolated by Diaion HP-20 adsorption chromatography, silica gel flash chromatography, recrystallization, and preparative HPLC. HPLC fractions corresponding to those two ginsenosides were recrystallized in appropriate solvents for the analysis of physico-chemical properties. Documentation of those isolated ginsenosides was achieved according to the method proposed by Gaedcke and Steinhoff. The ginsenosides were subjected to analyses of their general characteristics, identification, purity, content quantification, and mass balance tests. The isolated ginsenosides showed 100% purity when determined by the three HPLC systems. Also, the water content was found to be 0.534% for (20S)-Rg3 and 0.920% for (20R)-Rg3, meaning that the net mass balances for (20S)-Rg3 and (20R)-Rg3 were 99.466% and 99.080%, respectively. From these results, we could assess and propose a full spectrum of physico-chemical properties of (20S)- and (20R)-ginsenoside Rg3 as standard reference materials for GMP-based quality control.