Tumors originating from the nasolacrimal duct are exceedingly rare. Only a few cases have been reported previously. In advanced cases with extended tumor, differential diagnosis from lacrimal sac tumor is difficult. A 68-year-old Japanese man with intractable dacryocystitis was examined with intranasal endoscopy, computed tomography (CT) and magnetic resonance imaging (MRI). Squamous cell carcinoma extended from a medial site in the left orbit to the lacrimal orifice. En bloc resection was performed and histopathological examination of the surgical specimen using serial section suggested that the origin of the tumor was located in the nasolacrimal duct. This is the first case in nasolacrimal duct carcinoma whose differential diagnosis of origin has been studied in detail. We showed that pathological study using serial section along the duct provides useful information for diagnosing the tumor origin in addition to that obtained from imaging studies.