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OBJECTIVE The purpose of this study was to measure the 3-dimensional (3D) bone-to-implant contact (BIC) ratios calculated with an associated software algorithm on 3D micro-computed tomography (μCT) scans and compare them with measurements made with 2-dimensional histomorphometry. STUDY DESIGN For uncomplicated calculation of the 3D BIC ratios, 16 implants (8 grade 2 titanium and 8 grade 4 titanium) with simple cylindrical geometry were inserted into 8 rabbit tibiae; 2 implants were inserted into each tibia. The experimental animals were sacrificed at 2 weeks after surgery. The implants were surgically removed en bloc with surrounding bone. 3D μCT images were acquired and reconstructed, and histomorphometric procedures were performed. The calculated 3D BIC ratios were compared with the histomorphometrically measured BIC ratios. RESULTS When the 3D BIC ratios calculated in this study were compared with the BIC ratios measured conventionally by using histologic slides for light microscopy, no significant statistical correlation was found between the 2 ratios (P ≥ .35). CONCLUSIONS This study indicated that 3D μCT should be used for more accurate BIC assessment to produce an overall 3D picture for the bone-implant interface.