Arabidopsis RPS4 belongs to the Toll/interleukin-1 receptor (TIR)-nucleotide binding site (NBS)-Leu-rich repeat (LRR) class of disease resistance (R) genes. Like other family members in different plant species, RPS4 produces alternative transcripts with truncated open reading frames. The dominant alternative RPS4 transcripts are generated by retention of intron 3 or introns 2 and 3, which contain in-frame stop codons and lie downstream of the NBS-encoding exon. We analyzed the biological significance of these alternative transcripts in disease resistance by removing introns 2 and 3, either individually or in combination, from a functional RPS4-Ler (Landsberg erecta) transgene. Removal of one or both introns abolished the function of the RPS4 transgene, whereas expression was not affected. In addition, a truncated RPS4-Ler transgene encoding the putative TIR and NBS domains was not sufficient to confer resistance, suggesting that the combined presence of regular and alternative RPS4 transcripts is necessary for function. Interestingly, we observed partial resistance in transgenic lines expressing both intron-deficient and truncated transgenes. This finding confirms the requirement for regular and alternative RPS4 transcripts and indicates that alternative transcripts function at the protein level rather than as regulatory RNAs. Together with published results on the tobacco N gene, our data suggest that the generation of alternative TIR-NBS-LRR R gene transcripts is of general biological significance across plant species.