The replication of the hepadnavirus DNA genome is initiated by reverse transcription of pregenome RNA into minus-strand DNA followed by plus-strand DNA synthesis. The priming of plus-strand DNA requires the transfer of an RNA primer from pregenome RNA to the primer-binding site on minus-strand DNA. Annealing of the primer to the primer-binding site is facilitated by short direct repeats, DR1 and DR2. To investigate the mechanism of plus-strand primer formation, we have introduced specific mutations into DR1 and DR2 and measured the effect of these mutants on initiation of plus-strand DNA synthesis. To facilitate such an analysis, we have constructed a vector for the efficient expression of woodchuck hepatitis virus in cultured cells. Our results suggest that the 3' end of the RNA primer is determined prior to its transfer to the primer-binding site and that the determination of the 3' end of the primer does not depend on a specific sequence motif at the cleavage site. In addition, we have identified an alternative initiation site for plus-strand DNA synthesis at a purine-rich sequence between DR1 and DR2. Initiation at this site occurs by a mechanism that is independent of the direct repeats and does not require the transfer of an RNA primer to the primer-binding site.