Abstract An unknown heptabarbital metabolite, observed in the liquid chromatogram of rat plasma and urine samples after administration of heptabarbital, was identified by liquid chromatography-thermospray tandem mass spectrometry. By applying the parent scan mode for screening and the daughter scan mode for structure elucidation, the metabolite was determined to be 5-ethyl-5-(1′-3′- or 6′-cycloheptadienyl)barbituric acid. It was demonstrated that artefact formation occurred when hydrochloric acid was used for conjugate hydrolysis in the sample clean-up. Identification of the artefacts was achieved by the same method. Confirmation of the structures of the metabolite and the artefacts was obtained by gas chromatography-electron impact mass spectrometry.