Background: This trial study aimed to assess the effects of adenoidectomy on the markers of endothelial function and inflammation in normal-weight and overweight prepubescent children with obstructive sleep apnea (OSA). Methods: This trial study was conducted in Isfahan, Iran in 2009. The study population was comprised of 90 prepubescent children (45 normal-weight and 45 overweight children), aged between 4-10 years old, who volunteered for adenoidectomy and had OSA documented by validated questionnaire. The assessment included filling questionnaire, physical examination, and laboratory tests; it was conducted before the surgery and was repeated two weeks and six months after the surgery. Results: Out of the 90 children evaluated, 83 completed the 2-week evaluation and 72 patients continued with the study for the 6-month follow up. Markers of endothelial function, i.e., serum adhesion molecules including endothelial leukocyte adhesion molecule (E-selectin), intercellular cell adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (sVCAM-1), and the markers of inflammation, i.e., interleukin-6, and high-sensitive C-reactive protein (hsCRP) decreased significantly in both normal-weight and overweight children after both two weeks and six months. After six months, the total and LDL-cholesterol showed a significant decrease in the overweight children. Conclusions: The findings of the study demonstrated that irrespective of the weight status, children with OSA had increased levels of the endothelial function and inflammation markers, which improved after OSA treatment by adenoidectomy. This might be a form of confirmatory evidence on the onset of atherogenesis from the early stages of the life, and the role of inflammation in the process. The reversibility of endothelial dysfunction after improvement of OSA underscores the importance of primordial and primary prevention of chronic diseases from the early stages of the life.