The Clinical Institute was established on 1 January 2013. The institute is physically located adjacent to Aalborg University Hospital, where research, education and clinic are in direct connection with each other.

The Clinical Institute conducts research within the clinical specialties and also provides research-based teaching for all subject areas of the medical master's degree, and contributes to the master's degree in sexology. The Clinical Institute has affiliated around 40 research units, each with their own specialty. Many of the research units are organized in a number of interdisciplinary research collaborations within larger research areas, e.g. cardiovascular diseases, cancers and neurological conditions. Most units are affiliated with Region Nordjylland (e.g. via Aalborg University Hospital and Regionshospital Nordjylland), while some stand independently and exclusively as part of the Clinical Institute. This applies, for example, to the Center for General Medicine and the Center for RNA Medicine (Campus Copenhagen).