Resistance genes allow plants to recognize specific pathogens. Recognition results in the activation of a variety of defence responses, including localized programmed cell death (the hypersensitive response), synthesis of pathogenesis-related proteins and induction of systemic acquired resistance. These responses are co-ordinated by a branching signal transduction pathway. In tobacco, one branch activates virus resistance, and might require the mitochondrial alternative oxidase to operate. Here we discuss the evidence for this virus-specific branch of the transduction pathway and assess what must be done to further understand virus resistance and the role of the alternative oxidase in its induction.