The murine coronavirus mouse hepatitis virus (MHV) can cause a range of illnesses depending on the strain. These include hepatitis, enteritis, pneumonia, and encephalitis. Here we study the strains A59 and JHM. The A59 strain is weakly neurovirulent and causes moderate hepatitis. The JHM strain is highly neurovirulent, but is unable to replicate in the liver. Additionally, the immune response against CNS infections with JHM and A59 are different. In particular A59 induces a robust T cell response, while JHM induces a weak T cell response. We are interested in the genetic determinants of strain differences in virulence between A59 and JHM. Utilizing recombinant viruses we explored the roles of the following proteins on virulence: nucleocapsid protein (N), a multifunctional protein that when bound to RNA forms the viral nucleocapsid; internal (I) protein, a structural protein of unknown function expressed by A59, but not JHM; hemaglutinin-esterase protein (HE), a protein expressed by JHM, but not A59, that binds neuraminic acid and has acetylesterase activity. We demonstrate that differences in N have a major affect on neurovirulence. When the N of A59 is replaced with that of JHM the LD50 is reduced by approximately 1000 fold. This is associated with an increase in replication and greater antigen distribution in the CNS. In addition, expression of JHM N causes a minor decrease in the T cell response, but cannot account for the large differences in T cell response between A59 and JHM. Expression of A59 N by JHM did not confer hepatotropism nor did expression of JHM N by A59 block hepatotropism. N did appear to have a minor affect on hepatovirulence, as evidenced by a reduction of replication in the liver when A59 expresses JHM N. A recombinant A59 virus with a mutation in the I gene that abrogates expression had no affect on lethality of virus in the brain or liver, and a recombinant JHM virus with a mutation in the HE gene that abrogates expression had no affect on the lethality of virus in the brain after intracranial or intranasal inoculation.