The rate of change in bone density was not different between peri- and post-menopausal women. Differences in rate of change were observed in bone microarchitecture, specifically cortical porosity (Ct.Po), where peri-menopausal women increased +9% per year compared with the +6% per year for post-menopausal women. The purpose of this study was to compare changes in bone density and microarchitecture in peri- and post-menopausal women over 6 years. Peri- (n = 26) and post- (n = 65) menopausal women were selected from the Canadian Multicenter Osteoporosis Study. Caucasian women were scanned on dual x-ray absorptiometry (DXA) and high-resolution peripheral quantitative computed tomography (HR-pQCT) at baseline and follow-up, an average 6 years later. To compare repeat scans, automated 3D image registration was conducted. At the radius and tibia, total volumetric BMD (Tt.BMD), total bone area (Tt.Ar) and cortical porosity (Ct.Po) were assessed, and finite element analysis estimated apparent bone strength. At the tibia, the rate of change for Ct.Po and Tt.Ar was different between groups. Peri-menopausal women had a + 9% per year increase in Ct.Po, but this increase was slower for post-menopausal women at +6% per year (p = 0.049). In addition, post-menopausal women had an increase in Tt.Ar of +0.13% per year compared with a slower increase of +0.06% per year for peri-menopausal women (p = 0.017). The rate of change of density between groups was not significantly different and was approximately -1% per year at the hip by DXA, and -1% per year at the radius and -0.5% per year tibia by HR-pQCT. This is a 6-year prospective HR-pQCT study exploring rate of change in Caucasian peri- and post-menopausal women. The microarchitectural features represented by Ct.Po and Tt.Ar changed at a significantly different rate between groups, but group differences were not detected by density measures.