The aim of this work is to compare simultaneous isotope dilution analysis of organotin and organomercury compounds by gas chromatography-mass spectrometry (GC-MS) and gas chromatography-inductively coupled plasma mass spectrometry (GC-ICP/MS) on certified bivalve samples. These samples were extracted by microwave with tetramethylammonium hydroxide (TMAH). Derivatization with both NaBEt4 and NaBPr4 was evaluated, and analytical performances were compared. Two CRM materials, BCR-710 and CRM-477, were analyzed by both techniques to verify accuracy. A mixed spike containing (201)Hg-enriched methylmercury (MeHg), (199)Hg-enriched inorganic mercury (iHg), (119)Sn-enriched monobutyltin (MBT), dibutyltin (DBT), and tributyltin (TBT) as well as homemade (116)Sn-enriched monophenyltin (MPT), diphenyltin (DPT), and triphenyltin (TPT) was used for the isotope dilution analysis of samples. The two techniques studied were compared in terms of classic analytical parameters: linearity, precision or repeatability (i.e., percent relative standard deviation, RSD%), limit of detection (LOD), and limit of quantification (LOQ), showing excellent linearity, precision below 12% for all analytes, and LOQs of 0.06-1.45 pg for GC-MS and 0.02-0.27 pg for GC-ICP/MS.