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The study aims to examine drug-induced sleep endoscopy (DISE) in the decision-making process of pediatric obstructive sleep apnea (OSA) patients with small tonsils. This was a retrospective study of children who underwent awake flexible endoscopy, DISE, and adenoidectomy with/without tonsillectomy at the Shanghai Children's Medical Center between 03/2015 and 12/2016. Tonsillectomy was performed for tonsillar obstruction found by DISE. Adenoidectomy was performed for all children. Cardio-pulmonary coupling (CPC) and oximetry were observed before/after surgery. The study included 126 children: 56 (44.4%) with grade 2 tonsils and 70 (55.6%) with grade 1. Mean age was 5.7±3.2 (range, 2.8-10.4) years and mean BMI of 15.7±5.5 kg/m2. Unexpectedly, DISE showed tonsillar obstruction in 57 (45.2%) children, including 44 (78.6%) with grade 2 tonsils and 13 (18.6%) with grade 1. Therefore, DISE-directed tonsillectomy was performed for 57 patients. There was an improvement in respiratory disturbance index (RDI) and oxygen saturation nadir in the DISE (P = 0.0007, P = 0.037) and control (P = 0.001, P = 0.023) groups 6 months after surgery, but RDI improvement was better in the DISE group compared with controls 1 year after surgery (P = 0.042). DISE is a good way to determine the necessity of tonsillectomy in pediatric OSA patients with small tonsils.