The aims of this study were to test a locally applied carvacrol gel and determine its efficacy preventing alveolar bone loss in experimental periodontitis in rats by regular methodology to validate applicability the atomic force microscopy (AFM) as a novel morphology method on this model. Wistar rats were subjected to ligature around second, upper-left molars. Animals were treated carvacrol gel topically (CAG), immediately after Experimental Periodontitis Disease induction for 1' three-times/day for 11 days. A vehicle gel was utilized as control. The periodontium and the surrounding gingivae were examined at regular histopathology and by AFM method; the neutrophil influx into the gingivae was also assayed using myeloperoxidase activity. The bacterial flora was assessed through culture of the gingival tissue. Alveolar bone loss was significantly inhibited by CAG group compared to the Vehicle (V) group, the carvacrol gel treatment reduced tissue lesion at histopathology, with preservation of the periodontium, coupled to decreased myeloperoxidase activity in gingival tissue and also prevented the proliferation of periodontal microorganisms and the weight loss. The GAC treatment preserved alveolar bone resorption and showed anti-inflammatory and antibacterial activities in experimental periodontitis. Topographical changes in histological sections were seen bringing into high relief the periodontal structures, being a simple and cost-effective method for periodontal evaluation with ultrastructural resolution.