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This paper describes a simple, effective analytical procedure, based on a gas chromatographic mass spectrometric technique, for the speciation analysis of organotin compounds (OTC) in mussel samples. The direct alkylation reaction of the organotin chlorides in the aqueous digestion solution by NaBEt(4) allowed a short analysis time and a good recovery. The evaluation of the yield of each step constituting the analytical procedure indicated that the alkylation step is the most critical one. The proposed method was advantageously utilised to monitor the level of OTC pollution of the Lagoon of Venice. All the sites examined, both near to and far from anthropogenic activities, revealed significant levels of OTC pollution., (Copyright 2000 John Wiley & Sons, Ltd.)