Defects of the nasal septum occur as a result of a variety of causes, including tuberculosis, irritation, neoplasia, trauma, infection, and chronic inflammatory diseases. Congenital os vomer agenesis as a cause is very rare. We report the case of a 28-year-old man with a defect in the posteroinferior part of the nasal septum that was discovered incidentally during a routine endoscopic examination. The patient was diagnosed with congenital os vomer agenesis, and the diagnosis was confirmed by computed tomography. We discuss the features of this case and review the literature on this rare anomaly.