Traditional oriental medicines (TOM), with a very long history and many remarkable features, are very popular in Asian countries, especially in China, Japan and Korea. With the development of advanced analytical techniques, the modernization of traditional medicine has become a hot area in recent years and some herbal medicines have been increasingly accepted in western countries. Separation and determination of active components in various herbal medicines are considered to be critical for the modernization process. Antibacterial and antirheumatism agents are widely distributed in many medical plants and commonly used in clinical treatment. Therefore, the development of effective separation methods for the quality control of herbal medicines is absolutely important. In this article, the separation methods for the analysis of antibacterial and antirheumatism compounds in TOM were reviewed, including thin layer chromatography (TLC), gas chromatography (GC), supercritical fluid chromatography (SFC), high-performance liquid chromatography (HPLC), capillary electrophoresis (CE) and related hyphenation techniques. Sample preparation procedures and further development of these methods were also discussed.