Recently there has been increased awareness of the role of the carrier state in propagating Streptococcus equi var equi (S equi) infections (strangles), although the anatomical location of the organisms in chronic carriers has not been consistently established. This case report describes a chronic strangles outbreak in a riding school, that was monitored over six months by repeated clinical and endoscopic guttural pouch examinations. All asymptomatic horses that had positive S equi cultures on nasal swabs or guttural pouch lavages were found to have lesions in their guttural pouches. These lesions included empyema, chondroids and previously undescribed chronic discharging lesions on the floor of the medical compartment of the guttural pouches. These observations further support previous studies indicating the importance of investigating the guttural pouches in horses suspected to be asymptomatic carriers of this organism.