BACKGROUND: The objective of this study was to evaluate the clinical outcome of proton and carbon ion therapy for hepatocellular carcinoma (HCC). METHODS: In total, 343 consecutive patients with 386 tumors, including 242 patients (with 278 tumors) who received proton therapy and 101 patients (with 108 tumors) who received carbon ion therapy, were treated on 8 different protocols of proton therapy (52.8‐84.0 gray equivalents GyE in 4‐38 fractions) and on 4 different protocols of carbon ion therapy (52.8‐76.0 GyE in 4‐20 fractions). RESULTS: The 5‐year local control and overall survival rates for all patients were 90.8% and 38.2%, respectively. Regarding proton and carbon ion therapy, the 5‐year local control rates were 90.2% and 93%, respectively, and the 5‐year overall survival rates were 38% and 36.3%, respectively. These rates did not differ significantly between the 2 therapies. Univariate analysis identified tumor size as an independent risk factor for local recurrence in proton therapy, carbon ion therapy, and in all patients. Multivariate analysis identified tumor size as the only independent risk factor for local recurrence in proton therapy and in all patients. Child‐Pugh classification was the only independent risk factor for overall survival in proton therapy, in carbon ion therapy, and in all patients according to both univariate and multivariate analyses. No patients died of treatment‐related toxicities. CONCLUSIONS: Proton and carbon ion therapies for HCC were comparable in terms of local control and overall survival rates. These therapies may represent innovative alternatives to conventional local therapies for HCC. Cancer 2011;. © 2011 American Cancer Society. In this study, favorable clinical treatment results were demonstrated with both proton therapy and carbon ion therapy for hepatocellular carcinoma (HCC). Both therapies exhibited great advantages in treating HCC, a condition for which other local therapies are contraindicated. Thus, both proton therapy and carbon ion therapy may be innovative alternatives to conventional local therapies for HCC.