Abstract Objectives In radiographic axial spondyloarthritis (r-axSpA), spinal damage manifests as syndesmophytes and facet joint ankylosis (FJA). We evaluated whether the presence of one lesion increased the risk of the other lesion. Methods Patients with r-axSpA underwent low-dose CT (ldCT) and MRI of the whole spine at baseline and two years. On ldCT, vertebrae were scored for presence and size of syndesmophytes; facet joints were assessed for ankylosis. MR images were assessed for inflammation. Two hypotheses were tested: 1) presence of FJA is associated with new syndesmophyte(s) on the same vertebral unit (VU) two years later, and 2) presence of bridging syndesmophyte(s) is associated with new FJA on the same VU two years later. Two Generalized Estimating Equations models were tested per hypothesis using increase of FJA/syndesmophytes (model A) or presence of FJA/syndesmophytes (model B) as outcome, adjusted for inflammation at baseline. Secondary analyses tested the hypotheses with outcomes on adjacent VUs and dose-response effects. Results Fifty-one patients were included (mean age 49, 84% male, 82% HLA-B27+). Baseline bridging syndesmophytes occurred more often (range: 10–60% per VU) than FJA (range: 8–36%). ORs(95%CI) for presence of bridging syndesmophytes on development of FJA were 3.55(2.03–6.21) for model A and 3.30(2.14–5.09) for model B. ORs for presence of baseline FJA on new syndesmophytes were 1.87(1.20–2.92) for model A and 1.69(0.88–3.22) for model B. Secondary analyses yielded positive ORs for both hypotheses. Conclusions Bone formation in vertebrae and in facet joints influence each other’s occurrence, with the effect of syndesmophytes being larger than that of FJA.