Important aspects of modern skeletal research depend on the phenotypical characterization of trabecular bone microarchitecture as assessed by microcomputed tomography (micro‐CT). Until now, however, there have been no studies which compare the two most commonly utilized micro‐CT devices, namely, Skyscan and Scanco. The purpose of the current study was to examine the reproducibility and accuracy of these two micro‐CT devices in comparison to traditional histomorphometry in ovariectomized rats treated with either propranolol, salbutamol, or vehicle. 6 month old female Wistar rats were ovariectomized () or sham operated . OVX rats were divided into four groups and then subcutaneously injected with propranolol 0.1 mg/kg/day, propranolol 20 mg/kg/day, salbutamol 3 mg/kg/day, or vehicle for 10 weeks. At sacrifice, the left tibial trabecular bone microarchitecture was analyzed using both the micro‐CT Skyscan 1072 (ex vivo) and Scanco vivaCT40 (in vivo). Histomorphometric analysis was performed on the right proximal tibia. Comparisons between the different methods were performed using regression analysis, Bland‐Altman, Passing‐Bablock, and Mountain plots. Correlations were highly significant for all parameters measured between the two micro‐CT instruments and were less significant between histomorphometry and micro‐CT measurements taken from either the Skyscan or Scanco apparatus. Micro‐CT overestimated bone volume compared to histomorphometry. In the ovariectomized rat model, the two micro‐CT instruments revealed the same difference between groups whereas histomorphometry revealed only the difference which displayed the largest disparity between groups. In regards to the comparison between the two micro‐CT devices, Mountain plot methods indicated that BV/TV, BS/BV, and TbSp were equivalent, whereas a systematic bias was observed for TbN and TbTh. The authors were also able to describe the routine method used to determine the threshold between the two micro‐CT devices, which may help explain these differences. While some minor differences in the absolute values of the morphometry parameters exist between the micro‐CT measurements from the Skyscan and Scanco instruments, both of these devices display a high degree of accuracy and reproducibility.