High-throughput analyses are based on technologies characterized by their rapidity, simplicity, sensitivity, robustness, low cost and high efficiency. They offer the potential for screening a large number of samples per day, which cannot be done using classical methods. High-throughput analyses have shown their feasibility and efficiency in multidisciplinary fields such as drug screening, bioassays of compound against mycobacteria. Another successful application is based on direct introduction mass spectrometry for the analysis of very complex organic materials in petroleomics. High-throughput analyses appear to be very attractive in metabolomics, which aims to study the interface between the chemical universe and biology, to detect general metabolic disruptions induced by external factors through a metabolite profiling approach. In this review, we focus on high-throughput metabolomics using high resolution mass spectrometry (HRMS). Specifically, performances and limits of available analytical techniques dedicated to high-throughput analyses, including sample introduction methods, HRMS and data processing tools are discussed.