Background: The application of crop rotation systems may reduce the occurrence of soil-borne diseases by releasing allelochemicals and by subsequent microbial decomposition. Methods and Results: For reduction of ginseng root rot by the crop rotation system, after harvesting 6-year-old ginseng, fresh ginseng was grown along with continuous cultivation of sweet potato, peanut, and bellflower. Growth of 2-year-old ginseng was significantly inhibited in the continuous cultivation than in the first cultivation. Sweet potato, peanut and bellflower cultivations assisted in obtaining normal yields of ginseng in the first year after the harvest of 6-year-old ginseng. Salt concentration, potassium and sodium contents were gradually decreased, and, organic matter was gradually increased through cirp rotation. Phosphate, calcium and magnesium contents were not altered. The density of the root rot fungus was gradually decreased by the increase in crop rotation; however it was decreased distinctly in the first year compared to the second and third year. The severity of root rot disease tended to decrease gradually by the increase of crop rotation. Conclusions: Short-term crop rotation for three years promoted the growth of ginseng, however root rot infection was not inhibited significantly, although it was somewhat effective in lowering the density of the root rot pathogen.