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Apical periodontitis is usually diagnosed based on clinical findings and dental X-rays. Recently, however, dental cone beam computed tomography (CBCT), which provides 3-D images of the maxillofacial region, has enabled dentists to examine patients undergoing endodontic therapy more effectively, improving diagnostic accuracy. Here, we describe a positive treatment outcome achieved using CBCT to diagnose apical periodontitis of the maxillary premolars, which had proven difficult to diagnose based on clinical findings and dental radiography alone. The patient was a 42-year-old Japanese man who presented with the chief complaint of gingival swelling in the maxillary right premolar region. Our initial diagnosis, based on clinical findings and dental X-ray, was apical periodontitis of the maxillary right second premolar, and treatment was started. However, after the patient failed to respond to the treatment, CBCT was performed. Based on these new findings, the diagnosis was changed to one of apical periodontitis of the upper right first premolar, and the patient was treated accordingly. Previous studies have described the complex anatomical morphology of the upper premolars, noting multiple roots and variation in the morphology of the root canals. The 3-D images provided by dental CBCT allow better assessment of oral conditions than the traditional 2-D images provided by dental X-rays, which in turn enables the dentist to better select the most appropriate treatment. Here, the patient showed no symptoms and was progressing well at a 6-month follow-up visit. The present results indicate that when clinical findings and dental X-rays alone are insufficient to allow a secure diagnosis, CBCT offers an effective alternative which will enable the appropriate treatment to be selected more reliably.