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Background & Purpose Accurate radiographic assessment of secondary alveolar bone grafting (SABG) is critical in evaluating SABG outcomes in patients with cleft lip and palate. This study compared Periapical (PA) and Cone beam computed tomography (CBCT) grading of SABG outcomes and conducted an analysis of agreement rate between the two imaging modalities.Methods A retrospective chart review was performed of patients who underwent secondary alveolar bone grafting at a single institution. Bone quality of the alveolar cleft site was assessed at three root levels of the adjacent teeth on PA and CBCT images.Results 48 patients had pre- or post-operative images with both CBCT and PA that were appropriate for comparison. A total of 174 alveolar bone sections (three root levels of adjacent teeth in 58 pairs) were graded on CBCT and PA images. Agreement of CBCT grading with PA grading was 41.3% (72/174) overall. CBCT assessments rated bone quality lower than PA grading in 51.2% (89/174) of sections. CBCT had higher grading than PA image grading in 7.5% (13/174) of sections. The weighted Cohen Kappa value for comparison of CBCT and PA readings was 0.17, indicating a low rate of agreement. Wilcoxon signed rank test demonstrated that the difference between grading on CBCT and PA assessments was statistically significant (P< .001).Conclusions CBCT and PA readings demonstrated an overall low rate of agreement in the assessment of cleft alveolar bone. This investigation suggests that PA radiographs have lower sensitivity in detecting poor bone grafting outcomes.