Cystatins are endogenous and reversible inhibitors of cysteine peptidases that are important players in cancer progression. Besides their primary role as regulators of cysteine peptidase activity, cystatins are involved in cancer development and progression through proteolysis-independent mechanisms. Mechanistic studies of cystatin function revealed that they affect all stages of cancer progression including tumor growth, apoptosis, invasion, metastasis and angiogenesis. Recently, the involvement of cystatins in the antitumor immune responses was reported. In this review, we discuss molecular mechanisms and clinical aspects of cystatins in cancer. Altered expression of cystatins in cancer resulting in harmful excessive cysteine peptidase activity has been a subject of several studies in order to find correlations with clinical outcome and therapy response. However, involvement in anti-tumor immune response and signaling cascades leading to cancer progression designates cystatins as possible targets for development of new anti-tumor drugs. Display omitted •Cystatins are inhibitors of cysteine cathepsins.•Cystatins can act also via proteolysis-independent mechanisms.•Cystatins can be used as biomarkers for prediction of clinical outcome and therapy responses of cancer patient.•Mechanistic studies revealed that cystatins affect all stages of cancer progression.•Cystatins interfere with the antitumor immune response.