A new approach for the assay of rotenone (1) by isotope dilution mass spectrometry is presented. The extreme toxicity of rotenone, a natural phytodrug with insecticidal and piscicidal activity, recently banned by national and international environmental protection agencies, calls for the development of sensitive and accurate methods of analyses. Accordingly, the proposed protocol is based on the availability of the labeled internal standard rotenone-d3 (3) which can be conveniently prepared by consecutive and specific mono-O-demethylation, and remethylation with methyl iodide-d3. The sensitivity of the method is confirmed by the very low limit of detection (LOD) and quantitation (LOQ) values achieved in the assay of 1 in two distinct fortified matrices, and is further supported by the observed accuracy values.