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Purpose To assess bone microarchitecture in maxillary sites grafted with autogenous or xenogenous grafts as well as to demonstrate the usefulness of micro CT in dental implant research. Materials and Methods Samples ( n = 12) consisting of titanium fixation screws covered by at least 0.5-1 mm of human bone were obtained from 17 sites grafted with autogenous or xenogenous materials and prepared for micro CT scanning and conventional histology. Bone histomorphometric parameters were evaluated in three distinct regions (graft region, transitional region, and native bone region). Three-dimensional (3D) bone-to-implant contact ( BIC) calculation was performed using micro CT data. Histological sections were used to calculate two-dimensional (2D) BIC percentages, which were compared with values obtained from 2D micro CT images. Results Histomorphometric parameters varied according to the type of graft used, but sites reconstructed with autogenous bone showed higher mean values in general. In autograft samples, indices for parameters such as Tb.Th and Tb.Sp were significantly different when the native bone region was compared to the graft region. While a higher mean 3D BIC was found in the native bone region for both graft materials, significant BIC differences were absent when graft types were compared. The 2D BIC percentages obtained from histological and micro CT images were similar. Conclusions Autografts outperformed the xenogenous material used in this study concerning the histomorphometric parameters assessed. While graft type did not seem to influence 3D BIC, the native bone region showed the highest BIC percentages when compared to the other regions in both graft groups. In addition, 2D BIC ratios were similar regardless of graft material or image source (histological sections x micro CT slices). Taken together, our findings suggest that micro CT is an effective tool for 2D and 3D histomorphometric and BIC assessments in dental implant research. [ABSTRACT FROM AUTHOR]