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Objective: To reveal the factors affecting the incidence of chorda tympani nerve (CTN) transection during middle ear surgery. Study Design: Retrospective case review. Setting: Tertiary referral center. Patients We analyzed 232 ears (117 ears with cholesteatoma, 101 ears with chronic otitis media, and 14 ears with otosclerosis) that underwent tympanoplasty or stapes surgery during 2017–2020. Intervention: Eighty‐four ears underwent transcanal endoscopic ear surgery (TEES), 103 ears underwent microscopic ear surgery (MES), and 45 ears underwent surgery using both endoscopy and microscopy (Dual). Main Outcome Measure: To confirm CTN transection, intraoperative endoscopic/microscopic video images were evaluated. We used the same video images to determine the anatomical variation of the CTN course in the middle ear. Results: In 18 ears (7.8%: 6/84 TEES ears [7.1%], 6/103 MES ears [5.8%], and 6/45 Dual ears [13.3%]), the CTN was cut during middle ear surgery. There was no significant difference in CTN transection among groups. In cholesteatoma patients, stapes involvement resulted in a significantly higher CTN transection incidence. CTN anatomical variants such as the "Attached Short type" and "Ultrashort type" showed a significantly higher CTN transection incidence. Conclusion: Although endoscopic surgery did not reduce the incidence of CTN transection during middle ear surgery, pathological involvement of the stapes and CTN anatomical variants, such as the "Attached Short type" and "Ultrashort type," may increase this incidence. Preoperative evaluation of stapes involvement and anatomical location of the CTN course could help identify patients at greater risk for iatrogenic CTN transection. Level of Evidence: 4. [ABSTRACT FROM AUTHOR]