Most of the liver cell injury in hepatitis B and C infections is likely to be immune-mediated. Variation in the pathogenesis of these infections likely is contributed by a variety of host and virus factors. Host factors include the human leukocyte antigen (HLA) haplotype as well as the ability of the host to both recognize antigen on virus-infected cells and to receive the appropriate co-stimulatory signals in a timely fashion during infection. Virus factors include the genetic variation, direct cytopathic effects, and the alteration of infected hepatocytes to cytotoxic cytokines. The lack of suitable tissue culture systems and animal models limits the ability to understand the pathogenesis fully but provides challenges for their future development so that the basis for liver cell damage can be elucidated and approaches for therapeutic intervention can be achieved.