A palatal cleft can be reconstructed using various palatoplasty techniques. Many techniques use local mucoperiosteal flaps to close the hard palate cleft, without closing the underlying bone defect. The purpose of this study was to explore the possibility of spontaneous bone regeneration in the remaining bone defect following a two-stage palatoplasty. Furthermore, the effect of this bone regeneration on transverse maxillary growth was studied. A retrospective study of unilateral cleft lip and palate patients was performed. Cleft size was measured at the hard-soft palate junction on plaster models obtained during palatoplasty. Residual bony cleft was evaluated at the time of alveolar process reconstruction using CBCT images. The presence of crossbites was evaluated through clinical photographs to evaluate transverse maxillary growth. Forty-six patients were included in this study. Thirteen patients (28%) presented with complete ossification of the hard palate at the age of six years. Six patients (13%) had no ossification, while twenty-seven patients (59%) demonstrated partial closure, averaging 75% of the total hard palate length. All patients with complete closure and 89% of patients with partial closure presented without lateral crossbites. Statistical analysis revealed no significant correlation between lateral crossbites and the extent of hard palate ossification (p = 0.4314). 87% of children presented with at least partial ossification of the hard palate after a two-stage palatoplasty, indicating the potential for spontaneous bone regeneration. Importantly, lateral crossbites demonstrated no correlation with palatal ossification (p = 0.1819), suggesting no detrimental impact of regenerated bone on transverse maxillary growth.