Microtomographic techniques are widely used for studying the trabecular architectures in the orthopedics and elucidation of tooth micromorphology in the field of dentistry. Its application to assess the osseointegration of dental implants has been studied as a non-invasive method, contrary to several conventional methods. The aim of this study is to evaluate the possibility of microtomography as a tool for assessing osseointegration. Twenty-four titanium dental implants (3.75 mm in diameter and 7 mm in total length) were installed in the tibia of New Zealand white rabbits, and retrieved with the surrounding bone after 3 months. The specimens were analyzed by three-dimensional microtomogram images (Skyscan 1074) and compared with the conventional histomorphography. The correlation coefficient was found to be 0.855, which means the two data sources are significantly correlated statistically. To predict the histomorphometric data using microtomographic data, a linear regression model was applied. These results showed some promise of using microtomograms for non-invasive osseointegration assessment if the methods can be calibrated more precisely by further study.