Purpose: Drug induced sedation endoscopy (DISE) is performed to investigate patterns and sites of obstruction in patients with sleep-disordered breathing (SDB). During DISE the patients are sedated to obtain a muscular relaxation of the upper airway which mimics the relaxation during natural sleep. Different sleep stages are intended to be simulated by drug induced sedation, and it is helpful to measure the depth of sedation. The BiSpectral Index® (BIS) is often used for this procedure. Besides the BIS, other means of sedation depth monitoring exist in anaesthesiology but have not yet been investigated with respect to DISE. Monitoring of the Cerebral State Index® (CSI) is one of these methods. The aim of the study was to compare the BIS and CSI for sedation depth monitoring during DISE. Methods: Sixty patients underwent DISE monitored by the BIS and CSI in parallel. The BIS and CSI values were compared using the Bland-Altman analysis. Results: The BIS and CSI values differed during the course of sedation during DISE by a mean of – 6.07. At light sedation (BIS 60–80), lower values by 10 scale points of CSI compared with BIS were detectable. At deeper sedation levels (BIS 40–50), the CSI turned to present equal and even higher values compared with the BIS. Conclusion: Sedation depth measurement during DISE can be performed by the BIS or CSI, but the differences should be interpreted carefully as comparable data for sleep stages in natural sleep are available only for BIS.