Abstract: Rare diseases, with the characteristics of abundant species, low prevalence, and difficulty in diagnosis and treatment, have drawn more and more attention from our country in recent years. Usually, conventional laboratory tests can not meet the requirements for the diagnosis of rare diseases. Due to its high specificity, the ability of simultaneously differentiating and quantifying various metabolites, and so on, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has attracted wide attention in clinical laboratories, and been gradually moving from scientific research to the forefront of clinical practice. Based on the first batch of rare diseases published in China, we summarized in this study the status and prospect of LC-MS/MS in the clinical application of diagnosing rare diseases.