Panax Ginseng is a perennial medicinal plant originated from North-east asia. Because of its well-known tonic effects mainly from ginsenosides, various types of processed ginseng products have been distributed around the world. Here, we analyzed secondary metabolite profiling of adventitious roots of 5 korean ginseng cultivars, Chunpoong (CP), Sunhyang (SH), Gopoong (GO), Sunun (SU), and Cheongsun (CS). At the same time, the profiles of relative gene expressions related to ginsenoside biosynthesis pathway were compared among ginseng cultivars. Secondary metabolite profiles were revealed by UPLC/Q-TOF-MS from extracts of bioreactor derived adventitious roots of five ginseng cultivars. Using principal component analysis, secondary metabolite profiles of ginseng cultivars were categorized into three groups. Metabolites with high VIP values were annotated using known database and standards compounds. Relative gene expression of ginsenoside related gene were analyzed using realtime PCR. The three groups had distinct metabolite contents. Furthermore, gene expression profiles related to ginsenoside were also different, which might contribute diverse secondary metabolite composition of ginseng cultivars. Further integrated analysis would provide a relationship between genetic background of ginseng cultivars and secondary metabolite profiles.