The development of clinical signs of strangles in horses following immunization with a live attenuated vaccine can present a number of diagnostic challenges. Foremost from an epidemiological perspective it is important to ascertain if the infection was due solely to the modified live vaccine, reversion of the vaccine strain to wild-type, recombination between vaccine and wild-type strains or to recent infection with a wild-type strain. To answer these diagnostics challenges we utilized next generation sequencing to confirm that two cases of strangles in previously healthy yearling horses were caused by the vaccine strain. Both isolates recovered from the two cases of vaccine-related strangles contained 67 of the 68 mutations specific for the Pinnacle vaccine. Our data shed new light on the safety of this vaccine and suggest that factors beyond the maturity of the animal’s immune system can influence the development of post-vaccination adverse reactions in some horses