BackgroundDens invaginatus (DI) is a developmental anomaly arising from excessive proliferation or distortion of the enamel organ during tooth formation, often leading to the creation of a pocket or dead space within the tooth. This report presents a case of Type II DI in a maxillary lateral incisor with unique anatomy, diagnosed through cone-beam computed tomography (CBCT) and further analyzed with micro-computed tomography (micro-CT) post-extraction.Case presentationA 20-year-old male patient presented with recurrent pain and gingival swelling around the apex of tooth #22 for 12 months, unresponsive to antibiotic therapy. CBCT examination revealed a well-defined radiolucent area measuring approximately 10.3 x 9.9 x 7.0 mm at the apex of tooth #22, with an oval shape and distinct cortical border. The CBCT images confirmed that the invagination extended into the pulp chamber but did not reach the root apex. Based on these findings, a diagnosis of Type II DI with chronic apical periodontitis was established. The patient opted for extraction, and histopathological analysis of the apical lesion confirmed a periapical granuloma. Micro-CT analysis of the extracted tooth revealed that the invagination communicated with the external oral cavity via a pit in the crown and with the internal root canal system, serving as the conduit for pulp infection. Multiple apical accessory canals were identified, contributing to the persistent periapical infection and development of a periapical granuloma.ConclusionsThis case highlights the complexity of DI and the challenges in treatment due to its unique anatomical features. The report underscores the value of three-dimensional imaging techniques, such as CBCT, in the diagnosis and management of DI.