Micro fabricated delivery systems have shown promise in increasing oral bioavailability of drugs. Micrometer-sized polymeric devices (microcontainers) have the potential to facilitate unidirectional drug release directly into the intestinal mucosa whereby, drug absorption can be enhanced. The aim of this study was to develop an ex vivo model to investigate mucosal adhesion and orientation of microcontainers. Furthermore, to investigate how microcontainers with varying height, shape and material behave in regards to mucoadhesion and orientation. Microcontainers were placed at the top of an inclined piece of porcine small intestine. The tissue was perfused with biorelevant medium followed by microscopic examination to observe the orientation and amount of microcontainers on the tissue. The mucoadhesion of the microcontainers were evaluated based on the observed position on the tissue after being exposed to flow. When comparing the varying types of microcontainers, good adhesion was in general observed since most of the microcontainers were located in the beginning of the intestine. Microcontainers fabricated from the epoxy-based photoresist SU-8 had a slightly better adherence than those fabricated from poly-ɛ-caprolactone (PCL). The orientation of the microcontainers appeare to be dictated mainly by the height. In general, the model showed promising results in evaluating mucoadhesion and orientation.