GCSB-5 preparation is a purified extract from a mixture six herbal medicines (Acanthopanacis Cortex, Achyranthis Radix, Saposhnikoviae Radix, Cibotii Rhizoma, Glycine Semen Nigra, Eucommiae Cortex) that have been widely used in traditional medicine to treat various bone disorders. This study was carried out to obtain the HPLC analysis method that can be used to establish quantitative analysis of Glycine Semen Nigra and Eucommiae Cortex for standardization of GCSB-5 preparation. HPLC analysis methods for the simultaneous determination of genistin (Glycine Semen Nigra) and geniposide (Eucommiae Cortex) were established for the quality control of herbal medicinal raw material and preparation. And validation of HPLC analysis methods were conformed for verification of HPLC methods by check to specificity, linearity, intra-day precision, inter-day precision and accuracy following ICH guideline. As the result of quantitative analysis, the contents of genistin and geniposide in the raw material of GCSB-5 preparation were 0.0426-0.0427 mg/g and 0.431-0.432 mg/g. And GCSB-5 preparation contained genistin of 0.0202-0.0203 mg/capsule and geniposide of 0.211-0.212 mg/capsule, respectively.