The purpose of this study was to investigate the anatomical relationship between the lingual nerve and submandibular duct. This study included 1403 patients with submandibular or sublingual gland diseases who underwent intraoral removal of submandibular gland sialoliths, submandibular glands, or sublingual glands. Of all patients, 33 patients underwent bilateral surgeries. All surgeries were performed a single surgeon, and the anatomical relationship between the lingual nerve and submandibular duct was always identified intraoperatively and recorded in the operation recorded. The anatomical relationship was investigated based on the intraoperative findings. The lingual nerve which crosses above the submandibular duct was detected in 8 of 1436 sides (0.6%). There were 4 in the right sides and 4 in the left sides. The lingual nerve below the submandibular gland was seen in 99.4%. Although the lingual nerve crosses above the submandibular duct with a rarer incidence, surgeons should beware of injuring the lingual nerve during intraoral salivary gland surgery.