Objectives Compared with multirow detector CT (MDCT), specimen (ex vivo) micro-CT (mu CT) has a significantly higher (similar to 30 x) spatial resolution and is considered the gold standard for assessing bone above the cellular level. However, it is expensive and time-consuming, and when applied in vivo, the radiation dose accumulates considerably. The aim of this study was to examine whether the lower resolution of the widely used MDCT is sufficient to qualitatively and quantitatively evaluate bone regeneration in rats. Methods Forty critical-size defects (5mm) were placed in the mandibular angle of rats and covered with coated bioactive titanium implants to promote bone healing. Five time points were selected (7, 14, 28, 56 and 112 days). mu CT and MDCT were used to evaluate the defect region to determine the bone volume (BV), tissue mineral density (TMD) and bone mineral content (BMC). Results MDCT constantly achieved higher BV values than mu CT (10.73 +/- 7.84 mm(3) vs. 6.62 +/- 4.96 mm(3), p<0.0001) and consistently lower TMD values (547.68 +/- 163.83 mm(3) vs. 876.18 +/- 121.21 mm(3), p<0.0001). No relevant difference was obtained for BMC (6.48 +/- 5.71 mm(3) vs. 6.15 +/- 5.21 mm(3), p = 0.40). BV and BMC showed very strong correlations between both methods, whereas TMD was only moderately correlated (r = 0.87, r = 0.90, r = 0.68, p < 0.0001). Conclusions Due to partial volume effects, MDCT overestimated BV and underestimated TMD but accurately determined BMC, even in small volumes, compared with mu CT. Therefore, if bone quantity is a sufficient end point, a considerable number of animals and costs can be saved, and compared with in vivo mu CT, the required dose of radiation can be reduced.