Here, we describe a new BMV-based recombination system. It has been constructed in such a way that both tested RASes are placed in the same segment of the BMV genome (in the modified RNA3 molecule); therefore, we have called this system homomolecular. To prove the usefulness of the homomolecular system, we have employed it to examine the recombination activity of sequences derived from the hepatitis C virus (HCV) genome. The examined sequences have been inserted into RNA3 as direct or inverted repeats. This demonstrated that the 101 nt hypervariable region of HCV efficiently supports both homologous and non-homologous crossovers, while the most conservative 98 nt portion of HCV's 3 0 -UTR induces only non-homologous recombination events. Moreover, a direct comparison of the hetero-and homomolecular systems revealed crucial differences between the mechanisms of homologous and non-homologous recombination. The former involves preferentially two different segments of the BMV genome and the latter occurs more easily between the same genomic RNAs.