Bone wax, a haemostatic agent, is widely used in craniospinal surgical procedures for a long time, in spite of controversial results regarding its negative influence upon bone regeneration. In this experimental study, the effects of Ankaferd Blood Stopper (ABS), as an alternative haemostatic agent, were evaluated through histochemical, immunohistochemical and scintigraphic studies. The total of 30 adult female Wistar albino rats was randomly divided into three groups: intact control group (n = 10), bone wax group (n = 10), and ABS group (n = 10). Surgically, a 3.0 mm hole in diameter was drilled on the right side of calvarium of the rats using a Class Mini Grinder set in all three groups, as described previously. At the end of 8 weeks, bone healing and connective tissue alterations surrounding drilled calvarial defect areas of the rats were determined via haematoxylin and eosin and the Mallory's trichrome staining and anti-bone sialoprotein immunohistochemistry. Image Pro Express 4.5 programme was used for histomorphometric calculation of new bone and fibrotic tissue areas. All statistical analyses were made with SPSS 25.0 and analysis of variance (one-way ANOVA) followed by Bonferroni post hoc test was performed, p < 0.001 was considered as significance level. Histomorphometrically, it was found that he had the largest hole diameter and the least fibrotic scar area in the bone-wax group. In the bone wax group, it was observed that the material closed the hole and there was only a fibrotic scar tissue in the area between the bone tissue at the edge of the hole and bone wax, and a fibrotic tissue was formed in the bone wax area. During the histological procedure, this bone-wax material was poured and the sections were seen as a gap in this area. In the ABS haemostat group, the smallest hole diameter and the least fibrotic scar tissue were observed. Fibrotic scar tissue close to each other was found in the ABS haemostat and bone wax groups. Histological analysis of samples also showed a statistical significance for fibrotic connective tissue area between groups (p < 0.05). Scintigraphically, osteoblastic activity related to blood flow in the animal taken from the group with application of ABS haemostat was more pronounced compared to the other two groups. In our study, it has been concluded that the ABS yields affirmative effects on the bone healing, while bone wax leads to negative impact on the bone regeneration. Scintigraphic, histochemical and immunohistochemical data support the affirmative impact of the ABS haemostat application upon the bone regeneration apart from the quick stop of haemorrhage.