Molecular diagnostics in cancer aiming at improving diagnosis, prognosis and treatment are constantly exposed to new opportunities and challenges. The Belgian Commission of Personalised Medicine (ComPer-Med) has been created to advise the Federal Government on all matters related to personalised medicine in oncology, including the reimbursement of molecular tests. Here, we propose the Belgian strategy for molecular testing within a scientific based framework and its implementation in the Belgian healthcare system. For each tested biomarker a clinical test level is attached, which is key to establish the relevance of the test and to define the reimbursement.