Purpose: Phase-binning algorithms are commonly utilized in 4DCT image reconstruction for characterization of tumor or organ shape and respiration motion, but breathing irregularities occurring during 4DCT acquisition can cause considerable image distortions. Recently, amplitude-binning algorithms have been evaluated as a potential improvement to phase-binning algorithms for 4DCT image reconstruction. The purpose of this study was to evaluate the performance of the first commercially available on-line retrospective amplitude-binning algorithm for comparison to the traditional phase-binning algorithm. Methods: Both phantom and clinical data were used for evaluation. A phantom of known geometry was mounted on a 4D motion platform programmed with seven respiratory waves (two computer generated and five patient trajectories) and scanned with a Philips Brilliance Big bore 16-slice CT simulator. 4DCT images were reconstructed using commercial amplitude- and phase-binning algorithms. Image quality of the amplitude- and phase-binned image sets was compared by evaluation of shape and volume distortions in reconstructed images. Clinical evaluations were performed on 64 4DCT patient image sets in a blinded review process. The amplitude- and phase-binned 4DCT maximum intensity projection (MIP) images were further evaluated for 28 stereotactic body radiation therapy (SBRT) cases of total 64 cases. A preliminary investigation of the effects of respiratory amplitude and pattern irregularities on motion artifact severity was conducted. Results: The phantom experiments illustrated that, as expected, maximum inhalation occurred at the 0 amplitude and maximum exhalation occurred at the 50 amplitude of the amplitude-binned 4DCT image sets. The phantom shape distortions were more severe in the images reconstructed from the phase-binning algorithm. In the clinical study, compared to the phase-binning algorithm, the amplitude-binning algorithm yielded fewer or less severe motion artifacts in 37.5 of the cases (2464), comparable artifacts in 54.7 of the cases (3564), and slightly greater artifacts in 7.8 of the cases (564). Evaluation of SBRT cases demonstrated that the reconstructed tumor sizes and locations were comparable in 96 (128) of the MIP image pairs generated from both amplitude- and phase-binning algorithms. In this case the amplitude-binned image set rendered a smaller tumor size, which was likely due to very shallow respiratory amplitudes occurring over several breathing cycles. Conclusions: Overall, the amplitude-binning algorithm for 4DCT reconstruction reduced the severity of tumor distortion and image artifacts compared to the phase-binning algorithm. However, the full range of motion may not be characterized using amplitude-binning algorithms. Despite superior performance, amplitude binning can still be susceptible to motion artifacts caused by large variations in amplitude of respiratory waves.