Objective To develop consensus-based algorithms for genetic testing in patients with common craniofacial conditions. Design An online collaborative consisting of online meetings, independent work, and feedback across groups. Setting/Participants: A collaborative of genetics and pediatrics providers from three regional craniofacial centers (four institutions). Methods Collaborative participants agreed upon a shared initial framework, developed algorithms independently, and presented/tested the algorithms with a national audience. Algorithms were modified based on consensus feedback. Results The collaborative group developed final algorithms for genetic testing in patients with orofacial cleft, branchial arch conditions, and craniosynostosis. Conclusions Timely and accurate diagnosis of genetic conditions can support medical management recommendations that result in safer surgical interventions. Algorithms can help guide best-practices for testing, particularly in institutions without easy access to genetics providers.