Two cDNA probes (pRP60 and pRP80) were used to examine the hormonal regulation of expression of two cysteine endopeptidase genes in germinated whole seeds and de-embryonated seeds of rice. The pRP60 protein is a major rice cysteine endopeptidase named REP-1 that digests rice glutelin, the main seed storage protein. The pRP80 protein has features of a cysteine endopeptidase but has not yet been confirmed to be one. Neither mRNA was detectable in dry seeds, and the levels per seed increased sharply upon imbibition, reached peaks at d 6 to d 9, and then decreased. Both mRNAs were expressed in a seed-specific manner, but the accumulation of pRP60 mRNA was about ten times greater than the other. When seeds were de-embryonated and incubated, the amounts of both mRNAs were reduced to very low levels, but in the presence of 0.01 to 1 microM gibberellic acid (GA3) both again reached high levels. Addition of abscisic acid (ABA) or uniconazole, an inhibitor of gibberellin biosynthesis, partly eliminated the effect of GA3. Protein immunoblot analysis showed that the accumulation of the REP-1 protein in seeds was regulated by GA3 and ABA similarly to that of pRP60 mRNA, but the change in pRP60 mRNA with time after the onset of imbibition preceded that of the REP-1 protein.