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Gastrointestinal (GI) malignancies represent a wide spectrum of diseases of the GI tract and its accessory digestive organs, including esophageal (EC), gastric (GC), hepatocellular, pancreatic (PC) and colorectal cancers (CRC). Malignancies of the GI system are responsible for nearly 30% of cancer-related morbidity and approximately 40% of cancer-related mortality, worldwide. For this reason, the discovery of novel prognostic biomarkers that can efficiently provide a better prognosis, risk assessment and prediction of treatment response is an imperative need. Human kallikrein-related peptidases (KLKs) are a subgroup of trypsin and chymotrypsin-like serine peptidases that have emerged as promising prognosticators for many human types of cancer, being aberrantly expressed in cancerous tissues. The aberrant expression of KLKs in human malignancies is often regulated by KLK/microRNAs (miRNAs) interactions, as many miRNAs have been found to target KLKs and therefore alter their expression levels. The biomarker utility of KLKs has been elucidated not only in endocrine-related human malignancies, including those of the prostate and breast, but also in GI malignancies. The main purpose of this review is to summarize the existing information regarding the prognostic significance of KLKs in major types of GI malignancies and highlight the regulatory role of miRNAs on the expression levels of KLKs in these types of cancer.