Ayahuasca denotes an Amazonian psychotropic plant tea obtained from Banisteriopsis caapi, which contains beta-carboline alkaloids, chiefly harmine, harmaline and tetrahydroharmine. The tea usually incorporates the leaves of Psychotria viridis, which are rich in N,N-dimethyltryptamine (DMT), a psychoactive 5-HT 2A agonist. The beta-carbolines reversibly inhibit monoamine-oxidase (MAO), effectively preventing oxidative deamination of the orally inactive DMT and allowing its absorption and access to the central nervous system. Despite increased use of the tea worldwide, easy to perform and validated methods for its characterization do not exist and the metabolism and excretion of DMT and the beta-carbolines has not been studied systematically in humans following ayahuasca consumption. Thus, we developed a liquid chromatography electrospray ionization-tandem mass spectrometry procedure for the simultaneous quantification of the major alkaloid components of ayahuasca, including several known and potential metabolites. The assay was applied to a variety of ayahuasca samples and modified to be applicable to human blood and urine samples before and after consumption of ayahuasca. The major components present in ayahuasca samples were tetrahydroharmine and harmine, followed by N,N-dimethyltryptamine and harmaline. The major metabolite of DMT was the corresponding N-oxide, DMT-N-oxide which was found in both blood plasma and urine, although not detectable in ayahuasca samples. Less than 1% of the administered DMT dose was detected in urine or blood plasma, despite the inhibition of monoamine oxidase afforded by the presence of the harmala alkaloids in ayahuasca. The major harmala alkaloid excreted was tetrahydroharmine. The methods developed would be suitable for the study of ayahuasca in human and ethnobotanical research, as well as in forensic examinations of ayahuasca preparations. The characteristics of the methods suggest that their sensitivity, selectivity and reproducibility are adequate for use in further toxicological and clinical research on ayahuasca as well as functioning as an assay to screen biological samples for endogenous hallucinogens. Based on the results of these studies we also present a critical review of 69 published studies reporting the detection in human body fluids of three indole alkaloids that possess differing degrees of psychedelic activity. Suggestions for the future directions of ayahuasca and endogenous psychedelics research are offered.