Administration of molecular, pharmacologic, or cellular constructs to the intestinal epithelium is limited by luminal surface mucosal barriers and ineffective intestinal delivery via systemic injection. Many murine models of intestinal disease are used in laboratory investigation today and would benefit specific modulation of the intestinal epithelium. Our aim was to determine the feasibility of a modified microsurgical approach to inject the superior mesenteric artery (SMA) and access the intestinal epithelium. We report the detailed techniques for selective injection of the SMA in a mouse. Mice were injected with methylene blue dye to grossly assess vascular distribution, fluorescent microspheres to assess biodistribution and viral vector to determine biological applicability. The procedure yielded good recovery with minimal morbidity. Tissue analysis revealed good uptake in the small intestine and colon. Biodistribution analysis demonstrated some escape from the intestine with accumulation mainly in the liver. This microsurgical procedure provides an effective and efficient method for delivery of agents to the small intestine and colon, including biological agents.