Objectives This retrospective cross-sectional study aimed to present a new method for secondary alveolar bone grafting (SABG) assessment and to qualitatively evaluate the SABG results in unilateral cleft lip and palate patients. Materials and methods Research was conducted according to the STROBE guidelines. The study group consisted of 21 patients with a mean age of 16 years. High-resolution cone-beam computed tomography (CBCT) was performed at least 1 year after grafting. The experimental side was the cleft side, and the contralateral side without a congenital cleft was the control. Measurements were performed at four levels of the maxillary central incisors’ roots according to the new scale with scores from 0 to 3. The sum of the scores provided a general assessment of bone architecture. The Wilcoxon signed-rank test was used for intergroup comparisons, and a Kappa coefficient was used for reproducibility measurements. Results High individual variability was found, and the bone architecture was significantly worse on the cleft side than on the noncleft side. The results showed 28.57% failure, 33.33% poor, 19.05% moderate, and 19.05% good results from the surgical procedure. Kappa coefficients produced results from 0.92 to 1.00 for intra-rater and from 0.81 to 1.00 for inter-rater reproducibility. Conclusions CBCT provides detailed information about alveolar bone morphology. The new assessment method is useful at every treatment stage and provides excellent repeatability. SABG did not provide good bone morphology, in most cases. Clinical relevance This research presents a new universal alternative for the assessment of SABG by utilizing CBCT.