The aim of this study was to investigate the use of a gonadotrophin-releasing hormone (GnRH) vaccine in the treatment of headshaking in horses. Fifteen geldings received two doses of the GnRH vaccine four weeks apart. Serum was collected before and after vaccination to measure concentrations of luteinising hormone (LH) (10 horses) and follicle-stimulating hormone (FSH) (six horses). Owners recorded the frequency of seven common headshaking behaviours using a visual analogue scale (VAS) before vaccination and at two, four, eight, 12, 16 and 20 weeks after vaccination. Serum LH (P=0.008) and FSH (P=0.03) concentrations decreased significantly following vaccination. Although approximately one-third of the owners reported a subjective improvement in headshaking, serial scoring did not indicate a reduction in headshaking behaviours following vaccination with a commercial GnRH vaccine. Vaccination reactions were observed in four of 15 horses (27 per cent), including one case of severe, presumed immune-mediated, myositis.