Although an important index, the level of bone mineral density (BMD) does not completely describe fracture risk. Another bone structural parameter, the orientation of type I collagen, is known to add to risk determination, independently of BMD, ex vivo. We investigated the Haversian system of transiliac crest biopsies from postmenopausal women before and after treatment with parathyroid hormone (PTH). We used the birefringence of circularly polarized light and its underlying collagen arrangements by confocal and electron microscopy, in conjunction with the degree of calcification by high-resolution micro-X-ray. We found that PTH treatment increased the Haversian system area by 48.28±38.78%; decreased bright birefringence from 0.45±0.02 to 0.40±0.01 (scale zero to one, p=0.0005); increased the average percent area of osteons with alternating birefringence from 48.15±10.27 to 66.33±7.73 (p=0.034), decreased non-significantly the semi-homogeneous birefringent osteons (8.36±10.63 vs. 5.41±9.13, p=0.40) and birefringent bright (4.14±8.90 vs. 2.08±3.36, p=0.10) osteons. Further, lamellar thickness significantly increased from 3.78±0.11μm to 4.47±0.14μm (p=0.0002) for bright, and from 3.32±0.12μm to 3.70±0.12μm (p=0.045) for extinct, lamellae. This increased lamellar thickness altered the distribution of birefringence and therefore the distribution of collagen orientation in the tissue. With PTH treatment, a higher percent area of osteons at initial degree of calcification was observed, relative to intermediate-low degree of calcification (57.16±3.08 vs. 32.90±3.69, p=0.04), the percentage of alternating osteons at initial stages of calcification increasing from 19.75±1.22 to 80.13±6.47, p=0.001. In conclusion, PTH treatment increases heterogeneity of collagen orientation, a starting point to study the reduction in fracture risk when PTH is used to treat osteoporosis.