To compare the effective dose (ED) and image quality (IQ) of O-arm cone-beam CT (Medtronic, Minneapolis, MN, USA) and Airo multi-slice CT (Brainlab AG, Munich, Germany) for intraoperative-CT (i-CT) in spinal surgery. The manufacturer-defined protocols available in the O-arm and Airo systems for three-dimensional lumbar spine imaging were compared. Organ dose was measured both with thermo-luminescent dosimeters and GafChromic films in the Alderson RadiationTherapy anthropomorphic phantom. A subjective analysis was performed by neurosurgeons to compare the clinical IQ of the anthropomorphic phantom images acquired with the different i-CT systems and imaging protocols. Image uniformity, noise, contrast-to-noise-ratio (CNR), and spatial resolution were additionally assessed with the Catphan 504 phantom. O-arm i-CT caused 56% larger ED than Airo due to the high definition (HD) imaging protocol. The noise was larger for O-arm images leading to a lower CNR than that measured for Airo. Moreover, scattering and beam hardening effects were observed in the O-arm images. Better spatial resolution was measured for the O-arm system (9 lp/cm) than for Airo (4 lp/cm). For all the investigated protocols, O-arm was found to be better for identifying anatomical features important for accurate pedicle screw positioning. According to phantom measurements, the HD protocol of O-arm offered better clinical IQ than Airo but larger ED. The larger noise of O-arm images did not compromise the clinical IQ while the superior spatial resolution of this system allowed a better visibility of anatomical features important for pedicle screw positioning in the lumbar region.