Considerable progress in carotenoids research has been made to understand the carotenoid metabolism in animals including human. Epidemiological and clinical studies have correlated with dietary intake of carotenoids on reduction of vitamin A deficiency, age-related macular degeneration, cancer and cardiovascular diseases. Recent findings demonstrate the existence of carotenoid metabolites in vivo and their efficacy have made greater insight on prospecting carotenoid metabolites. Owing to their biological activity, exploration of analytical methods for the characterization of carotenoid metabolites is considered to be important before addressing the stability and bioactivity. Although few studies are available on carotenoid metabolites, their structural characterization in biological samples require a substantial refining of analytical protocols like isolation, purification, prerequisite of equipment parameters and robustness in hyphenated techniques.Recently, researchers have focused on biotransformation of carotenoids and made an attempt to screen their metabolites by high-throughput analytical strategies. However, till date there is no detailed analytical techniques available to fingerprint carotenoid metabolites, due to interference with complex biological matrices. This review highlights the carotenoid metabolism, possible bioconversion and available bio-analytical techniques to characterize metabolites in vivo. Further, advancement in sensitivity, mode of ionization and fragmentation patterns of metabolites were also discussed. The identification of carotenoid metabolites in system specific will have further insight in the emerging field of nutritional metabolomics.