This retrospective study compared the long-term results of percutaneous radiofrequency (RF) ablation for high-grade dysplastic nodules (DNs) and well-differentiated hepatocellular carcinomas (HCCs). Between April 1999 and December 2006, 20 patients with 21 high-grade DNs (range, 1.2-3.0 cm; mean, 1.9 cm) (group 1) and 49 with a well-differentiated HCC (range, 1.0-5.0 cm; mean, 2.3 cm) (group 2) underwent RF ablation. The technique effectiveness, local tumor progression, cancer-free and cumulative survivals using the Kaplan-Meier method were compared. The technique effectiveness rates at 1 year after RF ablation were 100% (19/19) and 94.1% (32/34) in groups 1 and 2, respectively (P > 0.05). The local tumor progression rates in groups 1 and 2 were 0% and 20.6% (7/34), respectively (P = 0.041). The local tumor progression in group 2 was seen on follow-up computed tomography 4-58 months (mean, 17 months) after RF ablation. The 1-, 3-, and 5-year cancer-free survival rates in groups 1 and 2 were 95.0% and 76.9%, 56.2% and 44.6%, and 38.5% and 24.8%, respectively (P > 0.05). The 1-, 3-, and 5-year cumulative survival rates in groups 1 and 2 were 100% and 97.9%, 73.0% and 68.0%, and 63.8% and 51.1%, respectively (P > 0.05). Percutaneous RF ablation is effective for treating high-grade DNs and well-differentiated HCCs. The long-term results after RF ablation of high-grade DNs may be improved compared with those of well-differentiated HCCs.