Inflammatory bowel diseases (IBD) are chronic relapsing inflammatory disorders involving the gastrointestinal (GI) tract, which arise from the confluence of genetic, immunological, microbial, and environmental factors. Clinical, genetic, and experimental data support the role of gut microbiota in contributing to the etiopathogenesis of these diseases. In IBD, the development of gut dysbiosis and imbalances in host-microbe relationships contribute to the extent, severity, and chronicity of intestinal inflammation. With continued advances in knowledge, technology, bioinformatics tools, and capabilities to define disease subsets, we will be able to lower risk and improve clinical outcomes in IBD through individualized interventions that restore host-microbial balance. This article provides a critical review of the field, based on the latest clinical and experimental information.