This is a review of the part played by the cysteine proteases in different physiological and pathological processes.Apoptotic processes have a crucial function in control of the number of cells in multicellular organisms, both during development and throughout life. Alterations in these are closely related to different pathological processes, from cancer (with fewer apoptotic processes) to the degenerative disorders in which apoptosis is increased. Although the stimuli which may induce apoptosis are very varied, the apoptotic phenotypes are similar. Different metabolic routes are involved in apoptosis and in these changes, both in transcription and postranscription. The latter form the basis of this paper. We review the role of the cysteine protease family, in which the caspases and calpains are the best representatives, which have been related to different degenerative models. In this review we describe the stimuli and cascades of intracellular signalling which occur on activation.These proteases are involved in many situations involving the development and maintenance of the number of cells in the tissues, both physiological and pathological. They may be considered to be possible therapeutic targets in neurodegenerative diseases such as Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease and Huntington's chorea.