Abstract Background Late and misdiagnoses of rare disease patients are common and often result in medical, physical and mental burden for the patient, and financial and emotional burden for the patient’s family. Low rare disease awareness among physicians is believed to be one of the reasons for these late and misdiagnoses of rare disease patients. The aim of this study was to investigate how information and education could be tailored to the needs and preferences of physicians in Belgium to increase their rare disease awareness and support them in diagnosing patients with a rare disorder. Nine exploratory interviews with Belgian rare disease experts were performed in December 2016 to help the development of a questionnaire on information needs of physicians and their consulted information sources in rare disease awareness and diagnosis. This online questionnaire was then completed by Belgian physicians (n = 295), including general practitioners (GPs), pediatricians and other specialists (i.e. neurologists, pediatric neurologists, endocrinologists and pediatric endocrinologists) during January and February 2017. Results Rare disease knowledge and awareness were the lowest among GPs and the highest among specialists. Interviewed experts indicated that physicians’ academic and continuous medical education should be focused more on “red flags” to increase rare disease attentiveness in daily clinical practice. GPs scored their academic education on rare diseases as insufficient but pediatricians and other specialists scored it significantly better (p < 0.001). Even though GPs declared to only need information on rare diseases when having a rare disease patient in their practice, specialists indicated to need more rare disease information in general. Most physicians confirmed that they had specific information needs regarding rare diseases. Unlike specialists, the majority of GPs were unaware of information sources such as Orphanet. Conclusion In order to effectively support physicians in Belgium to diagnose rare ...