Lysosomal cysteine proteinases, the cathepsins (Cats) belong to the papain family of proteinases, sharing a similar protein structure and mechanism of action. Subtle structural differences between these enzymes give rise to important variations in substrate specificity and specificity of inhibition by their endogenous inhibitors, the cystatins, stefins and kininogens under physiological and pathological conditions. Alterations in their expression, processing and localization have been observed at various levels in malignant human tumor tissue compared to normal and benign tissue counterparts. We have proposed that an imbalance between cathepsins and cystatins, associated with metastatic tumor cell phenotype, may facilitate tumor cell invasion and metastasis. The results of clinical investigations on cysteine cathepsins and their endogenous inhibitors in human breast, lung, brain and head and neck tumors, as well as in body fluids of ovarian, uterine, melanoma and colorectal carcinoma bearing patients, have shown that these molecules are highly predictive for the length of survival and may be used for assessment of risk of relapse and death for cancer patients. Their application for diagnosis, follow-up and the anticancer therapy has also been proposed.