OBJECTIVE The present study aimed at comparing clinical, radiographical, and histological findings in chronic periapical lesions such as cysts, granuloma, and abscess. METHODS The present study was conducted on 148 teeth having chronic inflammatory periapical lesions with or without nonsurgical endodontic treatment. Endodontic surgery was performed by single trained endodontist. After surgical endodontic treatment, biopsy sections of teeth were assessed histologically. All slides stained with hematoxylin/eosin and Gomori trichrome for light microscopy assessment. RESULTS Out of 148 teeth, 41 had chronic inflammatory lesions, 34 had inflammatory cysts, and 25 had indefinite lesions. Chronic inflammatory lesions assessed histologically found chronic apical periodontitis in 86 cases and inflammatory cysts in 62 cases. The difference was significant (P < 0.05). Out of 86 cases of chronic apical periodontitis confirmed clinical radiographically, 64% found positive, whereas 36% were not histologically. Out of 62 cases of inflammatory cysts confirmed clinically and radiographically, 78% found positive while 36% were not histologically. Out of 25 indefinite lesions, 56% found chronic inflammatory lesions while 44% found inflammatory cyst. CONCLUSIONS There was significant disagreement in clinical radiographic as well as histological diagnosis.