The identification of rare diseases with cardiovascular involvement poses significant diagnostic challenges due to the rarity of the diseases, but also due to the lack of knowledge and expertise. Most of them remain underrecognized and undiagnosed, leading to clinical mismanagement and affecting the patients’ prognosis, as these diseases are per definition life-threatening or chronic debilitating. This article reviews the cardiovascular involvement of the most well-known rare metabolic and endocrine diseases and their diagnostic approach through the lens of cardiovascular magnetic resonance (CMR) imaging and its prognostic role, highlighting its fundamental value compared to other imaging modalities.