It has been hypothesized that proteins modulate rapid eye movement sleep (REMS). Studies have shown an increase in the liberation of proteins in the mesencephalic reticular formation of cats during REMS. It has also been determined that protein-synthesis inhibitors diminish REMS and that protease-inhibitors increase this sleep phase. These and other studies support the importance of "di novo" protein molecules in sleep, and in particular, in REMS regulation. In this context, it is important to determine the role of endogenous proteases and their endogenous inhibitors in sleep regulation. In this study, we found that Cystatin C (CC), an endogenous protease inhibitor, diminishes wakefulness and increases REMS. We have also found an increase in CC expression after REMS deprivation and a tendency to decrease after a 2 h period of REMS rebound. We further showed that REMS deprivation increases the expression of Cathepsin H (CH), a protease inhibited by CC. These results suggest that naturally occurring protease-inhibitors enhance REMS, perhaps by facilitating the availability of proteins.