Although histology has proven to be a reliable method to evaluate the ossoeintegration of a dental implant, it is costly, time consuming, destructive, and limited to one or few sections. Microcomputed tomography (µCT) is fast and delivers three-dimensional information, but this technique has not been widely used and validated for histomorphometric parameters yet. This study compared µCT and histomorphometry by means of evaluating their accuracy in determining the bone response to two different implant materials. In total, 32 titanium (Ti) and 16 hydroxyapatite (HA) implants were installed in 16 lop-eared rabbits. After 2 and 4 weeks, the animals were scarified, and the samples retrieved. After embedding, the samples were scanned with µCT and analyzed three-dimensionally for bone area (BA) and bone-implant contact (BIC). Thereafter, all samples were sectioned and stained for histomorphometry. For the Ti implants, the mean BIC was 25.25 and 28.86% after 2 and 4 weeks, respectively, when measured by histomorphometry, while it was 24.11 and 24.53% when measured with µCT. BA was 35.4 and 31.97% after 2 and 4 weeks for histomorphometry and 29.06 and 27.65% for µCT. For the HA implants, the mean BIC was 28.49 and 42.51% after 2 and 4 weeks, respectively, when measured by histomorphometry, while it was 33.74 and 42.19% when measured with µCT. BA was 30.59 and 47.17% after 2 and 4 weeks for histomorphometry and 37.16 and 44.95% for µCT. Direct comparison showed that only the 2 weeks BA for the titanium implants was significantly different between µCT and histology (p = 0.008). Although the technique has its limitations, µCT corresponded well with histomorphometry and should be considered as a tool to evaluate bone structure around implants. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 101B: 1259–1266, 2013.