Metabolomics is the comprehensive analysis of small molecules involved in metabolic pathways that control biochemical processes and functions of cells in the body. Metabolomic studies consist of three major steps: pre-analytical, analytical and post-analytical. The review emphasizes the importance of the pre-analytical stage, which is the journey of a biosample from the patient to the biobank and then to the analytical laboratory. Based on the literature analysis, the review presents the factors that influence the quality of the sample and therefore the quality of the final research result: clinical information collection, biosample selection, biosample collection and processing, and subsequent storage. Proper design of metabolomic studies, quality control of samples from collection to analysis by physicochemical methods provides data that can improve the quality of disease diagnosis, provide a transition to personalized medicine.