In Arabidopsis, the NMD-defective mutants upf1-5 and upf3-1 are characterized by dwarfism, curly leaves and late flowering. These phenotypes are similar to those of mutants showing constitutive pathogenesis-related (PR) gene expression, salicylic acid (SA) accumulation and, subsequently, resistance to pathogens. The disease symptoms of upf1-5 and upf3-1 mutants were observed following infection with the virulent pathogen Pst DC3000 with the aim of determining whether the loss of nonsense-mediated mRNA decay (NMD) is involved in disease resistance. These mutant plants showed not only enhanced resistance to Pst DC3000, but also elevated levels of endogenous SA, PR gene transcripts and WRKY transcripts. UPF1 and UPF3 expression was down-regulated in Pst DC3000-infected Arabidopsis plants, but the expression of various NMD target genes was up-regulated. The expression of 10 defense-related genes was elevated in cycloheximide (CHX)-treated plants. The transcriptional ratios of eight of these 10 defense-related genes in CHX-treated to non-treated plants were lower in NMD-defective mutants than in the wild-type plants. These eight defense-related genes are possibly regulated by the NMD mechanism, and it is clear that an alternatively spliced transcript of WRKY62, which contains a premature termination codon, was regulated by this mechanism. Taken together, our results suggest that UPF1 and UPF3, which are key NMD factors, may act as defense-related regulators associated with plant immunity.