The L6 rust resistance gene from flax generates at least four transcript classes by alternative splicing of the third intron. The most abundant transcript class encodes a resistance protein containing domains that include nucleotide binding site motifs and a leucine-rich repeat region (NBS-LRR). The remaining three transcript classes encode truncated products which lack most of the C-terminal part of the protein containing the leucine-rich region (LRR). The four transcript classes occur in all plant organs examined and no induction of L6 expression was observed following infection of resistant plants with an avirulent rust strain expressing the corresponding A-L6 avirulence gene. Flax plants transgenic for an intronless L6 gene, incapable of encoding truncated resistance proteins by alternative splicing, expressed L6 resistance indistinguishable from that of the wild-type gene. Therefore, a definitive role for alternative transcripts and their predicted truncated products could not be assigned in the flax/flax rust system.