<p>Although organotin compounds are toxic, they are used in a variety of industries and have been recently found in trace levels in various marine products. A gas chromatography-mass spectrometry (GC–MS) analytical method for eight organotin compounds in marine products was established, and its effectiveness was confirmed through method validation and inter-laboratory reproducibility validation. Method validation was performed for matrix effect (ME), specificity, linearity, limit of detection (LOD), limit of quantification (LOQ), precision, and accuracy. The ME was found to be − 31.47 − 53.05% and matrix-matched calibration was performed for all matrices. Linearity was<i> r</i>² ≥ 0.999 for all matrices, and LOD and LOQ were 0.44 − 3.28 and 1.46—10.94&#xa0;µg/kg, respectively. Accuracy and precision in all matrices met the CODEX guidelines. The measurement uncertainty was estimated at 1.94 − 36.35% and complied with AOAC guidelines. The proposed analytical method was applied to 16 marine products and the total organotin compounds in these samples were found to be at the level of N.D. (&lt; LOD) − 25.09&#xa0;µg/kg d.w..</p> Graphical abstract <p></p>