Athens Medical School is one of the largest medical research institutions in Greece, where educational activities are combined with every-day practice in the University Hospital. The laboratories operating in the University Hospital produce a large amount of research material, mainly consisting of medical images and videos in digital format. In this paper, we present the Digital Library System built to support the collections of Athens Medical School laboratories. The system facilitates access through the Web to medical research material and on-line presentations/lessons. Laboratory collections have different requirement regarding digital material structure and metadata modelling. Thus, while designing the Digital Library architecture, the organisation and administration of dynamically created collections was explored. We introduced the term dynamic collection management to denote the support of automated collection definition and management within an integrated Digital Library environment. Laboratory staff is responsible for selecting the material to be added in the library, while they also participate in metadata creation. Furthermore, they use this material to create presentation or on-line tutorials, also stored in the Digital Library. To facilitate the aforementioned functionality the Digital Library system also supports a complex workflow environment.