The focus of this article is to provide a broad platform for original research and state-of-the-art reviews on novel or established proteomic, metabolomic, or transcriptomic biomarkers that contribute to the understanding of the underlying molecular mechanisms of rare diseases and/or that can be used for the diagnosis and prognosis of disease and individuals’ responses to therapies. The collection includes eight original research papers, one commentary, and six review articles from groups investigating biomarkers for a diverse range of rare diseases.