Carotenoid dietary intake and tissue levels in humans have been correlated with reduced incidence of various chronic diseases. However, there is scant knowledge regarding their metabolic fate and the true bioactive constituents. In addition to host factors, including genetic alterations such as single-nucleotide polymorphisms, the bioavailability of carotenoids depends largely on bioaccessibility (i.e. the solubility in the gut, which can be influenced by food matrix constituents such as lipids and fiber). A large fraction of unabsorbed carotenoids is passed on to the colon and it is unknown whether carotenoids can be further taken up or whether a significant proportion is fermented to unknown metabolites. This is important, as studies indicate that polar metabolites and/or derivatives appear to be bioactive, interacting with transcription factors such as NF-κB and Nrf2 and nuclear receptors such as RXR/RAR. While it is known that a fraction of carotenoids taken up by the enterocytes can be cleaved by beta-carotene oxygenases (BCO1/2) into apo-carotenoids, information about their further metabolism, biodistribution and excretion is scarce. In this chapter, a summary of current knowledge on factors influencing the fate of absorbed and non-absorbed carotenoids is attempted and health-relevant gaps in our understanding of their metabolism and degradation are highlighted.