The aim of this paper was to evaluate the usefulness of coupling digital image analysis with immunohistochemistry and histomorphometry data to the study of tissue response to hydroxyapatite in a model of critical size bone defect in calvaria of rats. A transosseous defect measuring 8 mm in diameter was performed with a surgical trephine in the parietal bone of 40 rats and divided into two experimental groups according to the treatment: group I (blood clot, control), group II (HA) and killed 1, 3, 6 and 9 months after implantation (n=5/group/period). The skullcaps with overlaying skin were collected and processed for paraffin embedding. The specimens were cut in the laterolateral direction into 5-µm thick semi-serial sections and stained with hematoxylin-eosin for identification and counting of polymorphonuclears cells, mastocytes, and multinucleated giant cells, MNG, or immunolabeled with anti- lysozyme, -factor VIII and –PCNA. Digital images were obtained and analyzed with the ImagePro-Plus® software for cell couting (polymorphonuclears cells, mastocytes, macrophages and MNG) and microvessel density. Image segmentation of anti-PCNA immunostaining was used for cell proliferation analysis. The digital images obtained allowed clear identification of cells of interest by through morphological aspects or immunostaining. Data recording and analysis was facilitated by the use of specific software for image processing and graphical and statistical analysis. It can be concluded that the techniques applied were usefull to identify and count cells, structures and process of interest making easier the effectiveness of hydroxyapatite in the critical size defect in rat calvaria model.