Tissue cryo-sectioning combined with Atomic Force Microscopy (AFM) imaging reveals that the nanoscale morphology of dermis collagen fibrils, quantified using the metric of D-periodic spacing, changes under the condition of estrogen depletion. Specifically, a new subpopulation of fibrils with D-spacings in the region between 56 and 59 nm is present two years following ovariectomy in ovine dermal samples. In addition, the overall width of the distribution, both values above and below the mean, has increased. The change in width due to an increase in lower values of D-spacings was previously reported for ovine bone; however, this report demonstrates that the effect is also present in non-mineralized collagen fibrils. A non-parametric Kolmogrov-Smirnov test of the cumulative density function indicates a statistical difference in the sham and OVX D-spacing distributions (p < 0.01).