As well as its museological functions, the Neanderthal Museum Foundation pursues a range of interdisciplinary scientific goals. Since its opening in 1996, the Neanderthal Museum has developed into a world-renowned research institution focusing on the early history of humankind. Not only is it involved in many international excavations, it also oversees NESPOS, the largest database of Ice Age archaeology in the world. At the same time the museum invests effort in building a network of lay researchers throughout the local region in order to boost local research into the Stone Age.
Furthermore, conferences and symposia are regularly held, which encourage transdisciplinary research and thinking. The results of these conferences and symposia are made available through the museum's own publication series.