Since the discovery of noncoding small RNAs such as microRNAs (miRNAs), and their roles as potential tumour suppressors or oncogenes, post-transcriptional and translational control of gene expression have become increasingly important in cancer research. Given that over a third of coding genes, as estimated by computational prediction, are regulated by miRNAs, various types of cancer will show direct association with changes in miRNA expression. The link of certain miRNAs with specific developmental stages, tissues and cancer contributes to their strong potential as biomarkers and novel therapeutic targets. In this review, we cover recent advances in miRNA research in human gastrointestinal cancer (colorectal, gastric, pancreatic and liver) and the potential of miRNAs as diagnostic and prognostic biomarkers.