Rare diseases are a serious public health problem that presents unique challenges to many countries. There is no internationally accepted definition for rare diseases. Patients suffering from rare cancers often face challenges, including late or incorrect diagnoses, difficulties finding clinical expertise and accessing appropriate treatments, and uncertainty in clinical decision making, with difficult and rare access for these patients to clinical trials. Treatment choice is difficult as little information is available in the literature. In such situations, clinicians will base treatment decisions on retrospective data or case report series with a lower scientific level of evidence than that obtained from randomised controlled clinical trials. The only way forward is clinical trials organisation, but to perform it within rare indications we are always faced with many methodological, regulatory, and organisational challenges, besides stakeholders’ different views, which are not usually concurrent. The aims of the European Organisation for Research and Treatment of Cancer (EORTC) are to develop, conduct, coordinate, and stimulate translational and clinical research in Europe to improve the management of cancer and related problems by increasing survival but also patient quality of life. In particular, extensive and comprehensive research in the field of rare cancers is beyond the means of individual European hospitals and can be best accomplished through the multidisciplinary multinational efforts of basic scientists and clinicians. In this paper, we will present an overview of the clinical research scene for rare cancers and will try to propose possible steps to improve the current situation.