Aim: To histologically evaluate the healing of intrabony periodontal defects treated with guided tissue regeneration (GTR), if it is combined with orthodontic tooth movement (OTM) or used as a sole treatment. Materials and Methods: Twenty subjects requiring regenerative periodontal therapy and OTM were treated with the use of extended, coronally advanced flaps according to the GTR techniques with the utilization of deproteinized bovine bone mineral (DBBM) particles. Patients either received early initiation of OTM (test) or had their teeth splinted (control) after the surgical intervention. Re-entry procedures were scheduled 9 months postoperatively to obtain a biopsy from the previous defect sites. The primary outcome variable comprised histological and histomorphometric analysis. Results: Control group cases (n = 9) revealed nice embedding of graft particles into newly formed bone, which were predominantly present in the central and apical third of the biopsy samples. The coronally located DBBM was more often encapsulated in the connective tissue. Test samples (n = 10), both at the tension and pressure sites, demonstrated incorporation of a reduced graft ratio into newly formed bone. Ongoing bone formation and the presumably orthodontic-induced remodeling also interfered with the bone substitute material. Histomorphometry showed a distribution of 17.4% versus 33.9% new bone (p = 0.011), 33.2% versus 16.3% graft ratio (p = 0.001) and 49.4% versus 49.7% soft tissue components (p = 0.74) in the control versus test groups, respectively. Conclusions: Early initiation of tooth movement does not appear to adversely affect periodontal bone healing. A pronounced graft reduction and new bone formation in test patients, compared to those in controls, occurred presumably due to the effects of orthodontic-induced bone remodeling.