Objective This study aimed to assess the quality of root canal fillings and the prevalence of periapical radiolucencies in the permanent teeth of 6-18 year-old Turkish children. Methods CBCT images of 150 patients' 235 teeth with a mean age of 16.0 +/- 2.06 years were included. Root development stage, quality of root canal filling, the presence and severity of periapical radiolucencies, and their relationship with anatomical structures were recorded. Correlations between the quality of root canal filling, periapical lesion, and lesion size were assessed using regression analyses. Results A total of 235 teeth (528 root canals) were evaluated. 65.5% of root canals had periapical lesions. Immature roots and mandibular teeth had the highest prevalence and the largest size of periapical radiolucencies (p < 0.05). Overfilling (n = 52), underfilling (n = 93), unfilled (n = 46), inhomogeneously filled (n = 113) root canals and poor coronal restoration (n = 85 teeth) were observed in terms of technical failures of endodontic treatment. The quality of endodontic treatment was associated with the presence of periapical lesion and lesion size (p < 0.05). Teeth with under-filled, overfilled or inhomogeneously filled root canals and poor coronal restoration had a periapical lesion larger than 5 mm (p < 0.05). Immature teeth were most associated with the presence of lesion (OR = 4.07) and the lesion size > 5 mm (OR = 3.71). Conclusion The prevalence of periapical radiolucencies in young permanent teeth showed an increase when the tooth was an incisor, had incomplete root development, or the root filling had technical errors.