Responses to Potato virus A (PVA, genus Potyvirus) segregate to three phenotypic groups in a diploid cross between Solanum tuberosum subsp. andigena and a highly interspecific potato hybrid. The aim of this study was to compare gene expression between the progeny genotypes which react with hypersensitive response (HR) to PVA, allow PVA accumulation in inoculated leaves but restrict PVA infection to the inoculated leaf by blocking systemic movement [non-necrotic resistance (nnr)], or are susceptible (S) and systemically infected with PVA. Expression levels of ca 10 000 genes were compared using probes arranged in a microarray format, and real-time RT-PCR was applied for quantitative comparison of the expression of selected defense-related genes (DRGs). Results showed that a few DRGs were autoactivated in HR genotypes at an early stage of plant growth in the absence of PVA infection, which was not observed in the two other phenotypic groups (nnr and S). More detailed studies on the DRGs encoding a beta-1,3-glucanase, a chitinase and a basic PR-1b protein showed that autoactivation of the genes was not evident in vitro and up to 2 weeks of growth in soil in a controlled growth cabinet but was apparent 2 weeks later. Hence, autoinduction of these DRGs in the HR genotypes could be associated with growth stage, environmental factors or both. Furthermore, a number of other DRGs were induced in the inoculated leaves of HR genotypes as a response to infection with PVA, which was not observed in nnr and S genotypes. These results provide some novel information about factors underpinning the higher levels of virus resistance realised in potato genotypes carrying virus-specific R genes and suggest that part of the resistance is attributable to additional 'minor' genes functioning simultaneously, hence adding to the overall responsiveness and level of resistance against infection. These results also imply that some genotypes might be more responsive to chemical induction of pathogen and pest resistance, which could be considered in screening of progenies in plant-breeding programs.