Aim: To investigate the association of Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3B (APOBEC3B, A3B) deletion with susceptibility to chronic Hepatitis B Virus (HBV) infection and occurrence, prognosis of HCC in Chinese population. Methods: In this retrospective case-control study, a total of 654 patients with chronic HBV infection and 249 healthy controls were recruited. All subjects were ethnic Han Chinese. The patients included 104 chronic hepatitis B (CHB), 263 liver cirrhosis (LC) and 287 hepatocellular carcinoma (HCC). The APOBEC3B (A3B) intact (I) and deletion (D) alleles were genotyped using polymerase chain reaction (PCR) method. Totally 243 HCC patients was followed-up and their clinicopathologic characteristics was collected. Results: Compared with the II genotype, the DD genotype was significantly related to a increased risk of HCC after adjusting for age, sex, smoking, and drinking (OR=1.95, 95% CI: 1.03-3.69). No significant association between A3B deletion and chronic HBV infection (P=0.121, after adjusted by age, sex, smoking and drinking). No significant differences were found in the frequencies of genotype and alleles of A3B deletion among HBV infection patients (patients with hepatitis B, patients with HBV-related cirrhosis, and HBV-related HCC). No significant differences were found between the overall survival of the A3B deletion genotype. Conclusion: Our study provides epidemiological evidence that the A3B deletion homozygosity mediate occurrence of HBV-related HCC in vivo.