Metabolome analysis involves the study of small molecules that are involved in the metabolic responses that occur through patho-physiological changes caused by genetic stimuli or chemical agents. Qualitative and quantitative metabolome analyses are used for the diagnosis of various diseases or chemical exposure. This article presents an overview of the different analytical methods available for performing the determination of the metabolome, including sampling, sample preparation and processing and interpretation of data. Critical comments are aimed at emphasizing the extraction methods as well as the biological samples used for metabolome analysis and data processing.