Abstract: Strangles that is caused by Streptococcus equi sp. equi is a highly contagious respiratory disease of horses. Prevention of the disease has been attempted using killed, protein extract-based and live genetically modified vaccines. The goal of this study is to characterize post-vaccinal complications following the use of an intranasal vaccine Pinnacle IN^TM, Fort Dodge Animal Health Animal Health, Overland Park, KS, USA. Horses residing farms in Colorado, Florida, Kansas, Kentucky, Minnesota and Ohio were examined. Fourteen S. equi isolates were cultured from various animals. Amplified Fragment Length Polymorphism (AFLP) was performed on the post vaccinal reaction isolates and the vaccine strain. Clinical signs in these post vaccinal reactions episodes included fever, localized neck abscesses or purpura hemorrhagica. DNA analysis showed that all of the post vaccinal reaction isolates that were obtained from various geographic locations were identical to the intranasal vaccine strain. These findings clearly suggest that the horses exhibited various clinical disease that is a result of vaccination.