A method for the solid-phase extraction (SPE) and liquid chromatographic–atmospheric pressure chemical ionization– mass spectrometric–mass spectrometric–isotope dilution (LC–APcI–MS–MS–ID) analysis of the indole hallucinogens N,N-dimethyltryptamine (DMT) and 5-methoxy DMT (or O-methyl bufotenin, OMB) from rat brain tissue is reported. Rats were administered DMT or OMB by the intraperitoneal route at a dose of 5 mg/kg and sacrificed 15 min post treatment. Brains were dissected into discrete areas and analyzed by the methods described as a demonstration of the procedure’s applicability. The synthesis and use of two new deuterated internal standards for these purposes are also reported.