Micro-Raman Spectroscopy is an efficient method for analyzing biological specimens due to its sensitivity to subtle chemical and structural changes. The aim of this study was to use micro-Raman spectroscopy to analyze chemical and structural changes in periodontal ligament after orthodontic force application and in gingival crevicular fluid in presence of periodontal disease. The biopsy of periodontal ligament samples of premolars extracted for orthodontic reasons and the gingival crevicular fluid samples collected by using absorbent paper cones; were analyzed by micro-Raman spectroscopy. Changes of the secondary protein structure related to different times of orthodontic force application were reported; whereas an increase of carotene was revealed in patients affected by periodontal inflammation.