An 18 month old Shire filly presented for a 2 month history of antibiotic responsive, malodorous, mucopurulent nasal discharge from her left nostril. Oral examination and standing endoscopy identified sinusitis with a necrotic mass in the ventral meatus, but no evidence of dental disease. Radiographs showed sinusitis on the left and a malformed left upper first molar (tooth 209). Given the patient's young age, and the inconclusive diagnosis, computerized tomography (CT scan) was performed which diagnosed an apical tooth root infection originating from abnormal tooth 209. The patient was taken to surgery, and the tooth was removed through a maxillary sinus flap. A communication was identified between the ventral meatus and ventral conchal sinus, allowing for substantial sinus drainage after surgery. This case study will discuss the diagnosis and treatment of an apical tooth root infection in a congenitally malformed tooth with the special considerations for dental surgery in young horses.