Purpose Accurate and effective registration of the vertebrae is crucial for spine surgical navigation procedures. Patient movement, surgical instrumentation or inadvertent contact with the tracked reference during the intervention may invalidate the registration, requiring a rapid correction of the misalignment. In this paper, we present a framework to rigidly align preoperative computed tomography (CT) with the intra-operative ultrasound (iUS) images of a single vertebra. Methods We use a single caudo-cranial axial sweep procedure to acquire iUS images, from which the scan trajectory is exploited to initialize the registration transform. To refine the transform, locations of the posterior vertebra surface are first extracted, then used to compute the CT-to-iUS image intensity gradient-based alignment. The approach was validated on a lumbosacral section of a porcine cadaver. Results We achieved an overall median accuracy of 1.48 mm (success rate of 84.42%) in ∼  11 s of computation time, satisfying the clinically accepted accuracy threshold of 2 mm. Conclusion Our approach using intra-operative ultrasound to register patient vertebral anatomy to preoperative images matches the clinical needs in terms of accuracy and computation time, facilitating its integration into the surgical workflow.