Functional endoscopic sinus surgery (FESS) is a recent addition to the treatment armamentarium of sinus disease. Performed through the nasal cavity using endoscopes and inciting no external scars, these advantages have renewed an interest in the surgical intervention of various sinus diseases. With minimal risk and complications associated with FESS, the temptation exists to lower the threshold and expand the indications for sinus surgery. However, regardless of the reduced risk, FESS should be pursued only when the goals are attainable and the limitations of surgery are understood for each specific disease. Chronic rhinosinusitis (CRS), affecting more than 31 million people a year, represents a treatment challenge. The challenge stems from evidence that CRS can result from different etiologies including bacteria, virus, fungi, superantigens, and unfavorable anatomy. With an unclear pathogenesis, success of medical therapy is often limited. Individuals failing medical therapy are candidates for surgical intervention. The controversy, indications, and goals of surgery in CRS are reviewed. Other indications for FESS are less controversial. Nasal polyps, which can interfere with medical therapy and obstruct airflow, often require surgical intervention. In addition, recent data has suggested a link between surgery and a reduction in inflammatory markers. Repair of skull base defects, and resection of benign and limited malignant nasal masses are also indications for FESS. This article reviews the indications of sinus surgery. In addition, it addresses some of the controversies, limitations, and advances in FESS.