In the context of cleft repair in animal research in rat models, different areas can be used for bone grafting. The aim of the present study was to present the tuberosity of the ischium as a new donor site and to evaluate its quality in relation to an artificial alveolar cleft. Four weeks after creating experimental alveolar clefts in seven Wistar rats, the repair was performed in the now twelve-week-old male animals using bone blocks grafted from the ischial tuberosity. Two days before surgery and two as well as twenty-eight days after surgery, microCT scans were performed, and the grafted bone blocks were analyzed regarding height, width, thickness, and volume. Additionally, bone mineral density (BMD) and bone volume fraction (BV/TV) were measured in the repaired cleft. The mean bone volume of the graft was about 19.77 ± 7.77mm. Immediately after jaw reconstruction the BMD and BV/TV were about 0.54 ± 0.05 g/cm and 54.9 ± 5.07% for the transplant and about 1.13 ± 0.08 g/cm and 94.5 ± 3.70%, respectively, for the surrounding bone. Four weeks later the BMD and BV/TV were about 0.57 ± 0.13 g/cm and 56.60 ± 13.70% for the transplant and about 11.17 ± 0.07 g/cm and 97.50 ± 2.15%, respectively, for the surrounding bone. A hip fracture was found in four of the animals after surgery. The ischial tuberosity offers large bone blocks, which are sufficient for cleft repair in the rat model. However, the bone quality regarding BMD and BV/TV is less compared with the surrounding bone of the alveolar cleft, even after a period of 4 weeks, despite recognizable renovation processes.