To evaluate the image quality and clinical implementation after setting modification of a three-dimensional isocentric C-arm fluoroscopic image intensifier system combined with a digital flatpanel detector as a new tool for sinus and petrous bone surgery. Image acquisition was performed using two cadaveric heads. Experimental design was oriented to the clinically sensible intraoperative setup. Different tube currents and orbital movements of the C-arm system were evaluated for image quality by three otolaryngological surgeons using predetermined landmarks. Modification of the X-ray intensity did not attain statistically significant values compared to the X-ray-intensity predetermined by producer (12.0-18.5 mA, p > 0.05) for either sinus or for petrous bone scans. Elliptical orbital movement resulted in significantly superior image quality than data sets acquired by circular orbital movement (3.194 vs. 2.809, p < 0.0001). New C-arm systems with 3D-capabiltity offer a promising tool for intraoperative near real-time image guidance. Image quality of the skull base can be improved significantly with optimized system settings.