We have previously reported cases of severe suprastomal stenosis after tracheostomy. In this observational study we investigated the occurrence of suprastomal stenosis as a late complication. Patients with persistent tracheostomy after intensive care underwent an endoscopic examination of tracheostoma, larynx and trachea. A percutaneous dilational tracheostomy was employed in 105 (71.9%) and surgical tracheostomy in 41 (28.1%) of the cases (n = 146). The incidence of severe suprastomal stenosis (grade II > 50% of the lumen) was 23.8% (25 of 105) after dilational tracheostomy and 7.3% (3 of 41) after surgical tracheostomy (p = 0.033). Age, gender, underlying disease, ventilation time, and swallowing ability were not significantly associated with the tracheal pathology. This study suggests that dilational tracheostomy is associated with an increased risk of severe suprastomal tracheal stenosis compared to the surgical technique.