The Pi-ta gene in rice (Oryza sativa L.) confers resistance to races of Magnaporthe oryzae B. Couch containing its cognate avirulence gene AVR-Pita. Pi-ta is a single-copy plant resistance (R) gene encoding a protein belonging to the nucleotide-binding site leucine-rich repeat (NBS-LRR) class. In the present study, we report alternative splicing events at the Pi-ta locus, the identification of new introns and novel differentially used splice sites associated with the Pi-ta gene. A total of 12 transcript variants were predicted with ORFs ranging from 945 to 3099 bp and encoding 11 distinct putative products between 315 and 1033 amino acids. Among them, five preserve complete NBS-LRR domains and two couple the original NBS-LRR domain of the Pi-ta protein with a C-terminal thioredoxin (TRX) domain. Gene expression analysis revealed that transcript variants encoding the TRX domain had, in a resistant Pi-ta containing rice variety, the highest level of expression in comparison to the other full length or truncated transcripts. These post-transcriptional modifications of Pi-ta produce a series of transcript isoforms that could have a significant role in the R gene regulation and/or may increase protein diversity. To our knowledge, this study represents the first report of alternative splicing of a CC-NBS-LRR gene producing truncated isoforms at both their 5′ or 3′ terminus and including transcripts with a TRX domain at their C-terminus.