In recent years, transnasal endoscopy had been more widely accepted for its safety and convenience, and although it can lead to a weaker pharyngeal reflex, compared with the effects of transoral endoscopy, examinees often suffer intolerable pain and discomfort during passage of the endoscope through the nasal cavity. The aim of this study was to estimate the relationship between the uncomfortable factors during transnasal endoscopy and nasal patency. The subjects comprised 23 consecutive patients who underwent transnasal endoscopy from October 2007 to April 2009 at our Gastroenterology and Otorhinolaryngology Departments. Immediately prior to endoscopy, the left and right nasal resistance was measured with an active anterior rhinomanometer; a value of 100 Pa was determined as nasal resistance. The transnasal endoscope was inserted in the subjectively preferred side by the examinee. Thereafter, the subjects were asked to fill in a questionnaire on physical tolerance during the procedure, to quantify the sensations of nasal pain, nausea, and choking on a 10-point visual analogue scale. The mean scores were 3.0 ± 2.7 for nasal pain, 1.7 ± 2.0 for choking, and 1.6 ± 1.9 for nausea. The most intolerable factor among the complaints was pain (45%), which was followed by nausea (18%) and choking (9%). Unilateral nasal resistance was significantly related with nasal pain only (P = 0.0135). In conclusion, the most difficult problem during transnasal endoscopy was pain, which was related to nasal patency. We successfully demonstrated the clinical significance of nasal patency in determining the side of insertion for transnasal endoscopy.