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Atrophic rhinitis (AR) is a chronic debilitating nasal mucosal disease of unknown aetiology and the definitive treatment is still elusive. This often leads to the patient suffering during the entire life span often depleting the individual psychologically. On the contrary, Rhinoscleroma (RS) for which the aetiology is clearly known and is completely curable has atrophic stage which is clinically indistinguishable from AR. Many cases of atrophic stage of RS are undetected and often they end up being treated as AR. This study was conducted to know the role of histopathology and other factors in differentiating AR and Atrophic stage of RS, which can significantly alter the course of treatment and outcome. Forty-five cases of clinically diagnosed AR were included in the study. Punch biopsy of nasal mucosa was obtained from the anterior end of inferior turbinate. Core culture was performed on one sample and histopathological examination for the other sample. Among the 45 patients, 38 (84.44%) of cases were diagnosed to be AR and 7 (15.56%) cases were diagnosed to be RS by histopathology. Core culture of RS subjects showed positive culture for Klebsiella rhinoscleromatis in five subjects (71%). To conclude, AR cases should be confirmed by histopathological examination to rule out RS, for effective management and to prevent complications.