Diagnosis of phacoanaphylactic endophthalmitis (or lens induced uveitis), a rare autoimmune disease, is difficult due to variable clinical presentation. We sought to diagnose a case based on the cytopathology of the anterior chamber aspirate. This is a case report of spontaneous phacoanaphylactic endophthalmitis in a 79-year-old woman with no history of eye trauma or surgery. After clinical examination, diagnostic anterior chamber paracentesis was performed. Cytologic examination of the aspirate revealed polymorphonuclear leukocytes, histiocytes, and plasma cells surrounding amorphous lens material. A mature cataract was removed subsequently, and the eye has remained free of inflammation postoperatively. As the clinical diagnosis of phacoanaphylactic endophthalmitis is often difficult, cytopathology of an anterior chamber aspiration specimen may be useful in diagnosing this rare, treatable condition. As far as we know, this is the first case report of the diagnosis of phacoanaphylactic endophthalmitis solely by anterior chamber fine needle aspiration biopsy.