A novel approach for the measurement of 37Cl, 81Br and 34S in organic compounds containing chlorine, bromine, and sulphur is presented to overcome some of the major drawbacks of existing methods. Contemporary methods either require reference materials with the exact molecular compositions of the substances to be tested, or necessitate several laborious offline procedures prior to isotope analysis. In our online setup, organic compounds are separated by gas chromatography (GC) coupled to a high-temperature reactor. Using hydrogen as a makeup gas, the reactor achieves quantitative conversion of chlorinated, brominated and sulphurated organic compounds into gaseous hydrogen chloride (HCl), hydrogen bromide (HBr), and hydrogen sulphide (H2S), respectively. In this study, the GC interface was coupled to a quadrupole mass spectrometer operated in single-ion mode. The ion traces of either H35Cl (m/z 36) and H37Cl (m/z 38), H79Br (m/z 80) and H81Br (m/z 82), or H232S (m/z 34) and H234S (m/z 36), were recorded to determine the isotopic ratios of chlorine, bromine, and sulphur isotopes. The conversion interface presented here provides a basis for a novel method for compound-specific isotope analysis of halogenated and sulphur-containing compounds. Rapid online measurements of organic chlorine-, bromine- and sulphur-containing mixtures will facilitate the isotopic analysis of compounds containing these elements, and broaden their usage in fields of environmental forensics employing isotopic concepts. Copyright © 2011 John Wiley & Sons, Ltd.