It is well established that bone is capable of adapting to changes in loading; however, little is known regarding how loading specifically affects the internal 3D microarchitecture of cortical bone. The aim of this study was to experimentally test the hypothesis that loading is a determinant of the 3D orientation of primary vascular canals in the rat tibial diaphysis. Left tibiae from 10 rats (30 weeks old) that had been immobilized (sciatic neurectomy) for 27 weeks, right SHAM-operated tibiae from these same rats (internal control) and right tibiae from 10 normal age-matched rats (external control) were scanned by micro-CT. Mean canal orientation (for the whole bone segment and by region), percent porosity, canal diameter and canal separation were quantitatively assessed in 3D. Canal orientation in the immobilized tibiae was significantly (P < 0.001) more radial (by 9.9°) compared to the external controls but did not differ from the internal controls (P = 0.310). Comparing the external and internal controls, orientation was significantly (P < 0.05) more radial in the internal control group (by 6.8°). No differences were found for percent porosity and canal separation. Canal diameter was significantly greater in the immobilized vs. internal (P < 0.001) and external control (P < 0.001) tibiae. The differences in orientation relative to the external controls indicated that the organization of cortical bone in the rat is affected by loading. Although the predicted difference in canal orientation was not detected between immobilized and internal control groups, the distributions of individual canal orientations, from which the mean values were derived, revealed distinctive patterns for all three groups. The internal controls exhibited an intermediate position between the immobilized and external controls, suggesting that paralysis on the contralateral side resulted in altered loading relative to the normal state represented by the external control. This was also evident in a regional analysis by quadrant. The loaded bones had the same cross-sectional shape; however, their internal structure differed. These results provide novel insights into the impact of loading on the 3D organization of primary cortical bone and have implications for understanding the relation between cortical bone adaptation, disease and mechanical properties.