Metabolomics can be significantly influenced by a range of pre-analytical factors, such
as sample collection, pre-processing, aliquoting, transport, storage and thawing. This therefore
shows the crucial need for standardizing the pre-analytical phase with the aim of minimizing the
inter-sample variability driven by these technical issues, as well as for maintaining the metabolic
integrity of biological samples to ensure that metabolomic profiles are a direct expression of the
in vivo biochemical status. This review article provides an updated literature revision of the most
important factors related to sample handling and pre-processing that may affect metabolomics results,
particularly focusing on the most commonly investigated biofluids in metabolomics, namely blood
plasma/serum and urine. Finally, we also provide some general recommendations and best practices
aimed to standardize and accurately report all these pre-analytical aspects in metabolomics research.