<p>Among plant proteases, cysteine papain-like endopeptidases such as ficin, bromelain, and papain occupy an important place due to their high proteolytic activity in the physiological pH range of the medium. The processes of thermal aggregation and autolysis of protease molecules can have a significant influence on their activity and, consequently, on the prospects of practical application. The mechanisms of aggregation of protein molecules are still insufficiently studied and it is still impossible to unambiguously predict their aggregation stability on the basis of their amino-acid sequence. In this connection, the aim of this work was to study the processes of thermal aggregation and autolysis of molecules of some cysteine proteases. It was found that despite the similar structural and functional properties of ficin, bromelain, and papain their thermal aggregation processes proceed with different intensities. In particular, ficin and bromelain are approximately comparable in terms of their aggregation stability, whereas papain is significantly less susceptible to aggregation processes when exposed to elevated temperatures. It is suggested that the presence and configuration of internal structures of the molecule, such as cavities, tunnels, and pores, as well as the charge properties of its surface, have a significant influence on the stability of these cysteine proteases to aggregation processes.</p>