Abstract: In recent years, molecular diagnostics has been the most promising branch of in vitro diagnosis(IVD) due to its high sensitivity and specificity. However, it’s not suitable for the research of molecule with macroscopic tools. Microfluidics can achieve precise control of micro-fluid and has been widely applied in molecular diagnostics because of its advantages such as lower sample consumption, shorter reaction time, and easier to integrate. Molecular diagnostics has made great development in methodology and automatic integration based on microfluidics. In this paper, we introduce the applications of microfluidics in molecular diagnostics and analysis the challenges of it.