In this study, we investigated the disease, insect damage, growth, and yield characteristics of sorghum and foxtail millet in an organic paddy-upland rotation system at Anseong-si Gyeonggi province, Korea, in 2016. Seven varieties of sorghum and foxtail millet are used in this study. A rotational upland field and continuously cropped upland field were compared in order to establish an optimum cultural method and to select the best sorghum and foxtail varieties for a paddy-upland rotation system. The incidence rate of major diseases was higher for sorghum than for foxtail millet. Moktaksusu (22.8%) had the highest incidence rate among sorghum varieties. Hwanggeumchal (7.0%) had the highest incidence rate among foxtail millet varieties. DS202 (89.3%) was the most severely damaged by Ostrinia furnacalis larva, which is the main pest of sorghum and maize. The weed numbers, and the weed fresh and dry weights were lower in the rotational upland field than in the continuously cropped upland field. Futhermore, the number of weed plants decreased by 42% and the dry weight of weeds decreased by 33% in the rotational upland field compared to the continuously cropped upland field. The culm length of sorghum and foxtail millet were 7.9 cm, and 3.4 cm longer, respectively, in the rotational upland field than in the continuously cropped upland field. The average yield of sorghum per 10 a increased by 90% in the rotational upland field compared to continuously cropped upland field. However, there was no significant difference between the rotational upland field and the continuously cropped upland field for foxtail millet. The most suitable varieties for a paddy-upland rotation system were judged to be Hwanggeumchal, Donganmae, and DS202 for sorghum, and Samdachal, Samdamae, Dahwangmae for foxtail millet.