The diagnosis of central nervous system tumours has been transformed in recent years from a microscopic morphology-based process to one dominated by the identification of somatic genetic alterations in tumour cells. This switch requires implementing radically different methods, for which appropriate training and financial resources must be allocated. The Canadian Association of Neuropathologists (CANP) has followed a process based on the scientific literature and consensus to develop recommendations for molecular testing of tumours of the brain and spinal cord, aiming to balance the need for treatment-determinant accurate diagnosis and the current limitations inherent in the transition to a new paradigm. The Professional Affairs Committee was charged with this task. A draft was discussed during the CANP general assembly, along with presentations from groups who had implemented molecular technologies, as well as others who relied on external laboratories. The Professional Affairs Committee summarised the consensus and submitted their recommendation to the CANP’s Executive Committee. A final report was posted on the CANP website for a month to allow all members to comment. The recommendations below apply to intrinsic tumours of the central nervous system and do not include metastatic disease or tumours impinging upon the nervous system from outside. These recommendations should be considered clinically relevant, as the results have direct consequences on the patient’s treatment, either through the use of targeted therapies or the trial-proven best application of radiation and/or chemotherapy.