Abstract In this paper, a new high-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICP-MS) methodology for the analysis of organotin compounds in complex matrices is described. Earlier studies had failed to show baseline resolution between dibutyltin (DBT) and triphenyltin (TPhT). The data presented in this paper show that, by using a different C-18 stationary phase material (Ace C-18) with decreased particle size, baseline resolution of DBT and TPhT can be achieved, with the resultant separation of a third interfering component. In addition, the Ace C-18 stationary phase yields a significant increase in the number of theoretical plates, and, combined with changes in the mobile phase composition, a reduction in run-time by ∼25%. It is shown that the minor compounds detected are present in the sample and not artefacts of the analytical procedure. The accuracy and precision of the proposed HPLC–ICP-MS method was demonstrated for the determination of TBT in oyster tissue during the BCR “MULSPOT” international interlaboratory certification project.