We evaluated the efficacy of pre-cryosurgery and post-cryosurgery circulating tumour cells (CTCs) as biomarkers for unresectable hepatocellular carcinoma (HCC). Real‑time qPCR was used to detect potential biomarker genes in CTCs, and magnetic-activated cell sorting (MACS) and fluorescence‑activated cell sorting (FACS) was performed on 47 patients with hepatocellular cancer who underwent cryosurgery. CTCs in the 47 patients were assessed 1 day before cryosurgery, and 7 and 30 days after cryosurgery. The number of CTCs was 17.70±5.725, 14.64±6.761 and 10.28±5.598, respectively, and this decreased significantly over time (P<0.01). ΔCt values for MAGE-3, survivin and carcinoembryonic antigen (CEA) were elevated significantly compared with those obtained before cryosurgery; 2-ΔΔCt values were <1 before cryosurgery, and were 0.63±1.56, 0.21±0.22 and 0.22±0.34 for MAGE-3, survivin and CEA, respectively, at 7 days after treatment. At 30 days after treatment, 2-ΔΔCt values for MAGE-3, survivin and CEA were 0.24±0.82, 0.03±0.07 and 0.02±0.08, indicating that gene expression in CTCs significantly decreased over time (P<0.01). CTCs were useful biomarkers for evaluating the efficacy of cryosurgery on unresectable HCC.