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Metabolomics is one of the most rapidly evolving of the omics sciences. For phenotyping individuals, it offers a promising platform that is needed for breakthroughs in biomedical and pharmacological research. A proper sample-pretreatment procedure is required for metabolomics studies to overcome the mismatch of the sample with the analytical method. Within the analytical workflow for metabolomics studies, sample pretreatment is important in order to obtain the meaningful, high-quality quantitative data needed to minimize inconsistencies between laboratories. In this review, we provide an overview of state-of-the-art sample-pretreatment techniques for mass spectrometry-based metabolomics. We pay attention to deproteinization, removal of interfering molecules, liquid-liquid extraction, solid-phase extraction, electromigration-based extraction methods and possibly emerging sample-pretreatment techniques for metabolomics. We give the advantages and the limitations of these techniques for metabolomics, and consider aspects such as automation and high-throughput analysis. Finally, we provide some conclusions and perspectives.