Purpose: To investigate the periapical tissue response after root end filling with intermediate restorative material (IRM) and filling of the root-end resection bone defects with autogenous bone or a bone graft substitute in comparison to empty controls. Materials and Methods: Vital roots of the second, third and fourth mandibular premolars in six healthy mongrel dogs were apectomized. The root canals were prepared and sealed with IRM following a standardized surgical procedure. The resection bone defects were either filled with autogenous bone (PB) or one of the bone graft substitutes; CERAMENTTM|BONE VOID FILLER, ChronOS?, TigranTM PTG, Easygraft? CLASSIC or left empty. After 120 days the animals were sacrificed and the specimens were analyzed radiologically and histologically. Kruskal-Wallis and Mann-Whitney tests were performed for statistical evaluation. Results: 34 sections were analyzed histologically. The evaluation revealed a variation in the outcome amongst the tested options, regarding reestablishment of the periapical bone healing and inflammatory infiltration in the sections. According to the tested variables, there was no statistical significant difference between the materials when comparing all groups as a whole. When comparing individual materials to each other there was statistical differences among some of the tested materials. Conclusion: The healing outcome after periapical surgery of a five-wall resection defect could not be increased by infill with autogenous bone or bone graft substitutes. The most important factor for the healing outcome in periapical surgery is the quality of the root-end sealing. The healing outcome after some of the tested bone substitutes, might be improved by longer healing time.