Carbon ion radiotherapy (CIRT) is unique as it possesses well-localized and superior-depth dose distribution in addition to less repairable radiobiological effects. The use of CIRT for various diseases has been explored as clinical trials at the Heavy Ion Medical Accelerator in Chiba (HIMAC), Japan. Since 1994, when the first clinical study of cancer therapy with carbon ion beams was started, about 50 clinical studies have been completed safely and effectively. These studies revealed that intractable cancers such as inoperable bone and soft-tissue sarcomas can be cured safely in a shorter overall treatment time, as can cancers in the head, neck, lung, liver, prostate, and postoperative pelvic recurrence of rectal cancer. The number of patients receiving CIRT has reached 6,000, and the therapy was approved as a highly advanced medical technology in 2003. Based on these experiences, we embarked on the research and development of new-generation beam delivery facilities such as a 3D scanning method with a pencil beam and a compact rotating gantry. Clinical research using pencil-beam scanning has been in operation since May 2011.