The potential benefits of proton therapy have been established in pediatric cancer, skull base tumor, uveal melanoma, and other types of cancers. Western and Asian countries, however, have differences in the pattern of cancer incidence; this leads to the difference in patient demographics for proton therapy. Furthermore, the advancement of the scanning beam technique in proton therapy greatly expands the capability of proton therapy in disease sites with great complexity. In this review, we focus on the cancers with high incidence in Taiwan, based on the Cancer Registry Annual Report, 2011, Taiwan. The potential case number and clinical benefits from proton therapy are evaluated and discussed. Two endemic cancers, hepatocellular carcinoma and head and neck cancer, are considered to be the major disease types appropriate for proton therapy in Taiwan. Primary lung cancer and left side breast cancer, which are popular in western countries as well as in Taiwan, are included for discussion. The issue of cost-effectiveness for proton therapy is also reviewed. Finally, we point out the clinical trials that should be conducted for proton therapy in Taiwan.