Clinical practice guidelines are useful tools for both patients and physicians. Several standardised operating procedures are in existence to describe tasks step by step to develop guidelines/recommendations. The end product consists of data synthesis from the systematic literature search and patient/physician’s inputs. For the prevalent diseases, the process for developing guidelines is straightforward; it is based on physicians’/patients’ experiences and abundance of the literature. When it comes to the realm of ultrarare diseases, there are few physicians who are familiar with a disease, and there is a scarcity of literature. In this viewpoint, we describe challenges from the methodological perspectives that occurred during the process of developing recommendations for autoinflammatory disorders with the goal of finding solutions that facilitate the development of guidelines for ultrarare diseases in the future.