Museum collections of biological specimens face several challenges for the future. How do we preserve all the information that a specimen bears for the upcoming generations? How do we make this information accessible to others, fellow researchers and the general public? 3D digitisation of the collection can be a solution to these problems. The Agora 3D project, a consortium of four Belgian federal institutions (The Royal Belgian Institute of Natural Sciences, The Royal Museum for Central Africa, The Royal Museum of Art and History and The Royal Institute of Cultural Heritage), evaluates and compares a set of digitisation techniques, already used on a regular basis by many universities and museums. Aside from the high end technologies like Computed Tomography (CT), µCT, 3D laser or structured light scanning, we also test inexpensive technologies like photogrammetry, Kinect technology, and Reflectance Transformation Imaging (RTI). The main objective is to determine which scanning technique is the most relevant depending on the different types and characteristics (e.g. size and materials) of natural history specimens by evaluating the data quality of the output, the time required for acquisition and post-treatment, the direct cost (equipment, staff and running costs), the ratio between automated and human work and finally the ratio between relevant scientific information and size of the 3D dataset. Agora 3D ultimately endeavors to develop a set of standards and protocols that can be used as guidelines by museums and universities to ensure optimal, cost-effective and readily applicable methodologies for the 3D digitization, definition of data formats, data storage, data analysis and visualisation.