<p>Purpose: This study assessed the prevalence of apical periodontitis (AP) and associated risk factors in healthy Saudi adults attending dental school at Najran university during the period from 2021–2024. Methods: CBCT scans from 420 healthy subjects (6,440 teeth) were reviewed. Data on AP prevalence, both overall and on untreated versus treated teeth, were collected. Scans were retrieved from the School of Dentistry at Najran university, spanning January 2021 to July 2024. Chi-square and multivariable logistic regression analyses were performed to investigate associations with risk factors such as gender, tooth type, root canal treatment adequacy, final restoration status, dental caries, and periodontal disease. Results: AP was diagnosed in 78.6% of subjects, with a per-tooth prevalence of 12.9%. AP was highly observed in root-canal treated teeth (42.9%) than in untreated teeth (7%). The highest odds of AP were associated with dental caries (OR = 239.8, 95% CI = 151.02–380.72) and endodontic mishaps (OR = 87.03, 95% CI = 38.14–198.64). Conclusion: This study found a high prevalence of AP among healthy Saudi adults attending dental school at Najran university from 2021 to 2024. Significant risk factors included dental caries, periodontal disease, molar teeth, inadequate endodontic treatment, and the absence of full-coverage crowns, while female gender was correlated to greater occurrence of AP. The strong association with dental caries and inadequate root canal treatment highlights the need for early intervention and preventive strategies to reduce the burden of AP.</p>