Metabolic fingerprint is a powerful tool in bioscience.It allows for better understanding of mechanisms of physiological and pathological reactions.Analysis of clinical samples provides not only information about individual response on the used treatment but also about medical condition of the patient.Although metabolomics gains its importance on scientific field sample preparation is still the main problematic step in entire process of metabolome analysis, which determine the quality of the studies.The use of solid-phase microextraction (SPME), particularly its in vivo format, enables the capture of a more representative metabolome and presents opportunities to detect low abundance, short-lived and/or unstable species not easily captured by traditional workflows.The technique is ideally suited for temporal, spatial and longitudinal studies of the same living system, as well as multi-compartmental studies of the same organism.SPME is useful for the investigation of biological systems ranging in complexity from cells to mammalian tissues.Several in-vivo SPME examples will be highlited the technique within the context of conventional sample preparation methods for metabolomics.