Vacuolar processing enzymes (VPEs) are responsible for the maturation of seed proteins. These processing enzymes belong to a novel group of cysteine proteinases with molecular masses of 37 to 39 kDa. We isolated two genes of VPEs from a genomic library of Arabidopsis. The gene products were designated alpha-VPE and beta-VPE, and they were 56% identical in terms of amino acid sequence. The amino acid sequences of alpha-VPE and beta-VPE were also 55% and 67% identical to that of castor bean VPE, respectively. The gene for alpha-VPE had 7 introns, while that of beta-VPE had 8 introns. Northern blot analysis revealed that alpha-VPE is expressed in rosette leaves, cauline leaves and stems of Arabidopsis, while beta-VPE is predominantly expressed in the flowers and buds. Neither alpha-VPE nor beta-VPE is expressed in the siliques. This result strongly suggests that the isolated genes encode isozymes of VPE that are specific to vegetative organs.