An effective vaccine is available for the hepatitis B virus (HBV), which is a very contagious human pathogen. The prevalence of chronic HBV infection is very low in the Netherlands (<0.5%), and no universal vaccination is in place. Instead, a program of vaccination for targeted groups at high risk of HBV exposure has been implemented. Because transmission of HBV can occur by various routes, the effectiveness of this targeted vaccination strategy is difficult to assess. Molecular typing data for the surface protein encoding gene of HBV isolates, in combination with epidemiological data, provide some insight into the main transmission routes. Due to the low mutation rate of the HBV genome, many isolates have identical S region sequences, which hampers phylogenetic analysis and identification of transmission chains. The molecular epidemiological analysis of acute HBV isolates based on the surface and core protein encoding regions were compared. The nucleotide diversity found in the C region was statistically significant greater (1.5 times) than in the S region, and phylogenetic analysis based on the C region showed a higher resolution. C region analysis resulted in an almost 50% reduction of genotype A isolates with identical sequences. C region analysis also indicated that no long-chain transmission of genotype D strains is occurring in the Netherlands, as all genotype D isolates have unique C region sequences. Defining the goals of molecular typing of HBV isolates should precede the choice for phylogenetic analysis on the basis of either C or S region sequences. J. Med. Virol. 80:233–241, 2008. © 2007 Wiley-Liss, Inc.