The CRANIRARE project aims to analyse the molecular and pathophysiological mechanisms of rare craniofacial malformations and to transmit the results into improved patient care. CRANIRARE will work on the molecular basis and gene identification of 12 selected rare craniofacial malformations. More than 850 patients including several large and unique families will be available for gene identification studies. Standardization and harmonization of clinical and molecular diagnosis, genetic counselling, and therapeutic strategies will be done using innovative ways, such as the implementation of a face-recognition software. The combination of different up-to-date methodologies will be used for gene identification, such as genome-wide array technologies for mapping and analysis of copy number changes, gene expression studies, and systematic candidate gene approaches based on functional analysis of signalling pathways. To improve future therapeutic options for patients with craniofacial malformations, we will develop novel technologies for local delivery of bioactive agents to induce bone tissue regeneration and test these technologies in cell systems and animal models. We have chosen to conduct this project CRANIRARE by integrating partners from different specialities and countries into a multidisciplinary approach. All partners have already proven their excellence in similar studies and are highly motivated to collaborate with each other and to exchange data, materials, and technologies. Clinical, genetic, and functional studies in the frame of CRANIRARE will subsequently lead to improved patient care. Different dissemination activities are planned and the partners will also focus on training of young scientists, both will further increase the sustained yield of the CRANIRARE project.