Nano-scale formulations are being developed to improve the delivery of orally administered medicines, and the interactions between nanoformulations and the gastrointestinal luminal, mucosal and epithelial environment is currently being investigated. The mucosal surface of the gastrointestinal tract is capable of trapping and eliminating large particles and pathogens as part of the natural defences of the body, it is becoming clearer that nanoformulation properties such as particle size, charge, and shape, as well as mucous properties such as viscoelasticity, thickness, density, and turn-over time are all relevant to these interactions. However, progress has been slow to utilise this information to produce effective mucous-penetrating particles. Areas covered: This review focuses on delivery method of nanomedicines both into and across the gastrointestinal mucosal surface, and aims to summarise the biological barriers that exist to successful oral nanomedicine delivery and how these barriers may be investigated and overcome. Expert commentary: Despite successes in the laboratory, no nanotechnology-enabled products are currently in clinical use which either specifically target the intestinal mucous surface or cross the epithelial barrier intact. New nanomedicine-based treatments of local diseases (intestinal cancer, inflammation, infection) and systemic diseases are advancing towards clinical use, and offer genuine opportunities to improve therapy.