Purpose Bleeding is one of the most challenging issues for surgeons performing endoscopic stapedotomy. During creation and elevation of the tympanomeatal flap (TMF) prevention or control of bleeding greatly facilitates the safety and comfort in the next steps of the surgery. The aim of this study was to compare the effects of cautery versus cold instrumentation during creation of TMF at endoscopic stapedotomy surgery. Methods We investigated 15 patients TMF created with cautery and 14 patients with cold instrument, and compared bleeding scores, operation time, postoperative hearing, pain and complications between groups. Results The mean bleeding score was significantly lower in cautery incised patients compared to cold instrument patients (1.2 +/- 0.9 vs. 2.3 +/- 1, p = 0.005). Mean duration of surgery was also significantly shorter in cautery used patients (35.3 +/- 6.8 vs. 48.8 +/- 9.2 min, p < 0.001). There was no significant difference between postoperative pain, complications, wound healing, and auditory outcomes. Conclusions Cautery may be a better choice for the creation of TMF in endoscopic stapedotomy surgery due to reduced bleeding, shorter operation time and increased comfort without causing any complications.