We investigated the frequency and the clinical relevance of hepatitis B virus (HBV) pre-S mutations in Qidong, China. The results showed HBV pre-S mutants were detected in 48.4% (47/97) of patients with HBV infection. Both pre-S deletion and pre-S2 start codon mutations were more frequently found in HCC than in CH patients (51.1% vs. 18.0%, P < 0.01 and 21.2% vs. 8.0%, P = 0.06). In most cases, pre-S mutants coexisted with the wild-type HBV strain. Longitudinal observation clearly revealed that in four of five cases, HBV deletion mutants emerged during the course of HBV infection and eventually became the predominant or exclusive viral population at the stage of HCC. Thus, it was concluded that HBV pre-S mutations were highly prevalent and closely related to HCC in Qidong. Our results also provided direct evidence that pre-S deletion mutants were not acquired from the beginning of infection but arose de novo during the progression of liver disease.