Collagen, a naturally birefringent biopolymer and key structural component of the periodontal ligament (PDL), is altered substantially with regard to its molecular cross-linked structure by the dietary lathyrogen, beta-amino-proprionitrile (beta-APN). Our purpose in studying beta-APN-fed animals was to learn if the strength of birefringence of periodontal collagen, measured microscopically by the Senarmont compensator method, correlates with the molecular changes known to occur in these lathyritic animals, and to explore this technique for the periodontal ligament. Five experimental animals were fed a diet containing 0.25% beta-APN for two weeks, and 3 control animals were fed normal rat chow. Tissues were decalcified and the mandibular incisors were cut in cross section at 4 microns and stained with eosin Y. The Senarmont compensator, an attachment for the polarizing microscope, was used to measure phase retardation. Ten measurements were taken from each of the three sides (mesial, lateral and lingual) of the triangularly shaped incisor sections. The collagen fibers of the beta-APN-fed rats had lower values of phase retardation than the controls (p < 0.001), indicating reduced molecular organization. In addition, minor but significant regional differences were revealed, supporting the method for structural studies on the periodontal collagen.