A reliable method for the determination of iodine and molybdenum in milk samples, using alkaline digestion with tetramethylammonium hydroxide and hydrogen peroxide, followed by quadrupole ICP-MS analysis, has been developed and tested using certified reference materials. The use of He + O2 (1.0 ml min−1 and 0.6 ml min−1) in the collision-reaction cell of the mass spectrometer to remove 129Xe+ – initially to enable the determination of low levels of 129I – also resulted in the quantitative conversion of Mo+ to MoO2+ which enabled the molybdenum in the milk to be determined at similar mass to the iodine with the use of Sb as a common internal standard. In order to separate and pre-concentrate iodine at sub μg l−1 concentrations, a novel method was developed using a cation-exchange column loaded with Pd2+ and Ca2+ ions to selectively retain iodide followed by elution with a small volume of ammonium thiosulfate. This method showed excellent results for aqueous iodide solutions, although the complex milk digest matrix made the method unsuitable for such samples. An investigation of the iodine species formed during oxidation and extraction of milk sample digests was carried out with a view to controlling the iodine chemistry.