Background Measurement of selenium in serum is an important clinical biomarker of nutritional status. The presence of gadolinium (Gd) in samples following administration of the contrast agents used for magnetic resonance imaging (MRI) results in a significant positive bias when using quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS). Methods Three instrumental set-ups were assessed: standard mode with no collision gas and collision cell mode with either a hydrogen:helium mixture or hydrogen. The effect of Gd on the selenium (Se) signal was assessed using external quality assurance (EQA) specimens and internal quality control (IQC) materials, both unspiked and spiked with Gd. Serum previously shown to contain high concentrations of Gd-containing contrast agents were also analysed. Results Recoveries of Se in the spiked compared to the unspiked samples were: between 500% and 1300% using standard mode; 100% and 29,000% using collision cell mode with hydrogen:helium mixture; and between 99% and 103% using hydrogen. The use of H₂ in the collision cell provided accurate results, indicating that the charge exchange reaction (CER) of Gd²⁺ with H₂ removes this interference. Analysis of patient serum known to contain the Gd contrast agent using the method gave results within the selenium reference range (adults 0.89–1.65 µmol/L). The presence of Gd, as low as 0.2 mg/L, in serum samples causes a positive interference on the measurement of Se by ICP-MS. Conclusions Using a CER mode with pure H₂ in the collision cell it was possible to fully remove the interference due to Gd²⁺ from the signal for Se.