MicroRNAs (miRNAs) are small noncoding RNAs that are implicated in gene expression regulation at both a transcriptional and at a translational level. Single-nucleotide polymorphisms may occur in miRNA biogenesis pathway genes, primary miRNA, pre-miRNA, or a mature miRNA sequence. Such polymorphisms may be functional with respect to biogenesis and actions of mature miRNA. These single-nucleotide polymorphisms may have a potential to affect the efficiency of miRNA binding to the target sites or can create or disrupt binding sites. The resulting gene dysregulation may involve changes in phenotype and may eventually prove critical for the susceptibility to inflammatory bowel disease and its onset. In this review, we summarize their importance as candidate inflammatory bowel disease biomarkers.