Purpose: Images from computed tomography (CT), combined with navigation systems, improve the outcomes of local thermal therapies that are dependent on accurate probe placement. Although the usage of CT is desired, its availability for time-consuming radiological interventions is limited. Alternatively, three-dimensional images from C-arm cone-beam CT (CBCT) can be used. The goal of this study was to evaluate the accuracy of navigated CBCT-guided needle punctures, controlled with CT scans. Methods: Five series of five navigated punctures were performed on a nonrigid phantom using a liver specific navigation system and CBCT volumetric dataset for planning and navigation. To mimic targets, five titanium screws were fixed to the phantom. Target positioning accuracy (TPECBCT) was computed from control CT scans and divided into lateral and longitudinal components. Additionally, CBCT-CT guidance accuracy was deducted by performing CBCT-to-CT image coregistration and measuring TPECBCT-CT from fused datasets. Image coregistration was evaluated using fiducial registration error (FRECBCT-CT) and target registration error (TRECBCT-CT). Results: Positioning accuracies in lateral directions pertaining to CBCT (TPECBCT=2.1±1.0mm) were found to be better to those achieved from previous study using CT (TPECT=2.3±1.3mm). Image coregistration error was 0.3±0.1mm, resulting in an average TRE of 2.1±0.7mm (N=5 targets) and average Euclidean TPECBCT-CT of 3.1±1.3mm. Conclusions: Stereotactic needle punctures might be planned and performed on volumetric CBCT images and controlled with multidetector CT with positioning accuracy higher or similar to those performed using CT scanner