Purpose Assessment of bony fusion following anterior cervical interbody fusion (ACIF) is usually done by plain film or CT. We present the first clinical application of Cone-Beam CT (CBCT) to evaluate bony fusion after ACIF. Methods A 56-year-old man with disc herniation at C6-C7 underwent ACIF surgery using a compressed nanocrystalline hydroxyapatite interbody device (nanOss-C, Pioneer Surgical Marquette, MI, USA) and a nanocrystalline hydroxyapatite bone graft filler (nanOss Bioactive, Pioneer Surgical Marquette, MI, USA). Imaging follow-up was performed by CBCT (NewTom 5G, QR Srl, Verona, Italy) at 1 day, 6 weeks, 3 and 9 months postoperatively. Two independent assessors quantitatively measured the greyscale changes of the bone graft filler and qualitatively evaluated the bony fusion process. Results Quantitative analysis of the images showed a steadily increasing matrix density of the bone graft filler over the 9 months follow-up, suggesting increasing calcification. Qualitative evaluation demonstrated different stages of the bone fusion process within the disc space around the cage, at the interface between cage and endplates, and at the interface between bone graft filler and the endplates.Conclusions CBCT provides high-resolution cross-sectional imaging of the cervical spine after ACIF. For the first time, in vivo evaluation of the bone graft filler within the centre of the circumferentially radiodense cage and detailed cross-sectional evaluation of bone fusion was achieved. Confirmation of these promising outlooks of CBCT in a large cohort of ACIF patients is needed with regard to routine clinical application and evaluation of different interbody devices.