The RNA-dependent RNA-polymerase, 3D(pol), is an essential component in the picornavirus genome for the replication of single stranded RNA. However, transgenic expression of 3D(pol) in mice has antiviral effects. Here we discuss the structure and function of 3D(pol) during picornavirus replication, we review the evidence and consequence of a host immune response to epitopes in 3D(pol) after picornavirus infection, highlight data showing the antiviral effects of transgenic 3D(pol) from Theiler's murine encephalomyelitis virus (TMEV), and discuss potential mechanisms by which 3D(pol) is causing this antiviral effect in mice.