Background: Percutaneous cryoablation has been increasingly utilized for hepatocellular carcinoma (HCC) treatment. Long-term percutaneous cryoablation results have not been well described, especially in comparison with surgical resection. Methods: One-hundred patients with 1-3 HCC tumors <5 cm in diameter from Zhangjiagang Hospital Affiliated to Soochow University and Huai'an First People's Hospital, Nanjing Medical University were enrolled into this study. Among them, 49 patients were treated by cryoablation and 51 were treated by hepatectomy. Follow-up examinations were performed for the first four weeks after treatment, then every three months for the first 24 months and every six months thereafter. Results: One-, two-and three-year overall survival rates were 96.1%, 88.2% and 62.7% for hepatectomy, respectively, and 89.8%, 77.5% and 51.0% for cryoablation, respectively (P=0.179). One-, two-and three-year disease-free survival rates were 94.1%, 62.7% and 25.4% after hepatectomy, respectively, and 85.7%, 51.0% and 18.3% after cryoablation, respectively (P=0.185). Subgroup analyses indicate that patients with tumors <= 3 cm had significantly better survival rates compared with patients with tumors >3 cm (P=0.003). Neither patients with <= 3 cm tumors nor patients with >3 cm tumors exhibited survival differences when treated with either resection or cryoablation (P=0.095 and P=0.282, respectively). Patients with single tumors exhibited significantly better survival rates than patients with multiple tumors (P<0.001). No significant differences were observed in the survival rates of either single or multiple tumor patients treated with resection or cryoablation (P=0.851 and P=0.780, respectively). Tumor diameter, number and Child-Pugh scores were significant prognostic factors for overall survival. Conclusion: Percutaneous cryoablation and hepatectomy were equally effective HCC treatments.