At the end of September 2000, clinical symptoms of Bluetongue appeared in sheep flocks of the Balearic Islands (Spain). The presence of the BTV serotype 2 in tissue and blood samples of affected animals was confirmed by laboratory techniques. A systematic vaccination were carried out in affected areas using a live monovalent serotype 2 vaccine available from Onderstepoort laboratory (South Africa). In order to perform epidemiological studies, a new method to differentiate between the NS1 genes of BTV-2 affecting the Balearic islands and that of the Onderstepoort commercial live virus vaccine (monovalent, serotype 2) has been developed. This procedure is based on the use of an RT-PCR, followed by restriction endonuclease analysis. Epidemiological data of a study carried out in the period January-October 2001 using this procedure are included.