Objective To investigate the accumulation of mutations and single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) might be associated with cancer risk and disease outcome. Methods We obtained cancerous and noncancerous liver tissues from 49 HBV-related HCC patients at the Fourth Hospital of Hebei Medical University. mtDNA of the liver tissues was extracted with Mitochondrial DNA Extraction Kit. Mutation and polymorphism were confirmed by repeated analysis. We assessed the prediction power of D-loop SNPs in hepatocellular carcinoma (HCC) patients. Results No mutation in these HCC patients had prediction power for post-operational survival, whereas one SNP site (nucleotide 150 C/T) was identified by the log-rank test for statistically significant prediction of HCC survival. In an overall multivariate analysis, allele 150 was identified as an independent predictor of HCC outcome. The length of survival of patients with allele 150C was significantly shorter than that of patients with allele 150T (relative risk, 0.246; 95% CI, 0.070-0.861; P=0.028). Conclusions The analysis of genetic polymorphisms in the mitochondrial D-loop helps to identify patient subgroups at high risk of a poor disease outcome.