This study aimed to measure the prevalence of untreated root canals and periapical lesions in endodontically treated teeth using cone-beam computed tomography (CBCT) and their association with the coronal seal.This cross-sectional study assessed CBCT images of studied patients alongside documented information from their dental examinations. The assessment method for analyzing CBCT images after including endodontically treated teeth was the presence of missed canals, and periapical lesions were analyzed in three dimensions.The evaluations from 772 teeth demonstrated that 89.4% of teeth had the proper coronal seal, 13.3% owned missed root canals, and 29.4% had periapical lesions. Most untreated canals belonged to maxillary first molars (71.8%) and mandibular lateral incisors (33.3%). The prevalence of periapical lesions was highest in mandibular lateral incisors (58.3%) and maxillary second molars (55.8%). In teeth with missed canals, the most periapical lesions were observed in the first premolars of both jaws. In teeth with the lack of proper coronal seal, the periapical lesions were observed in 55.6% of teeth with untreated root canals.The results revealed a high prevalence of missed canals and periapical lesions in endodontically treated teeth in our study population.