The aim of this study was to compare the two in vitro culture systems callus and adventitious root by investigating the biomass and phenolic compounds in calli and adventitious roots induced from four different explants (leaf, root, petal, and ovary) in Camellia japonica. The biomass of calli and adventitious roots was examined after 4 and 8 weeks of cultivation, respectively, and 22 phenolic compounds were analyzed using high-performance liquid chromatography (HPLC). The biomass of the ovary-derived calli (2.0 g･mass-1) was 1.5-fold that of the leaf-derived calli. The dry weight (DW) was highest in ovary-derived calli; however, the highest dry matter content was obtained from leaf-derived calli. Differences in the investigated characteristics depended on the callus origin. In adventitious roots, the highest biomass was achieved in the leaf-derived adventitious root system; its fresh weight was 2.3-fold (89 mg･ea-1) higher, and its DW was 1.8-fold (16 mg･ea-1) higher than those of ovary-derived adventitious root system. Active cell division was detected in petal-derived lines in both the calli and adventitious roots. Results of the HPLC analysis revealed that the total content of 22 phenolic compounds was highest in ovary-derived calli and ovary-derived adventitious roots. Our experiments confirmed that the calli and adventitious roots of C japonica have different cytological characteristics and bioactive compounds depending on the explant origin. In addition, callus culture was a more suitable system than adventitious root for producing phenolic compounds when the duration of the culture period and biomass were considered.