A prospective cohort study aimed to assess the inhibitory effect of cigarette smoking on the rate of periapical bone healing after root canal treatment (RCT). Examination included both clinical and radiographic parameters to define healing status at baseline, 6 months, and 1 year after RCT. To examine and compare the healing rate of apical periodontitis (AP) after RCT between smokers and nonsmokers, and to evaluate how the intensity and duration of smoking affect AP healing up to 1-year follow-up. Study hypothesis was that smoking habits could delay or deteriorate AP healing. The study protocol was approved by the local ethics committee and all of the participants signed a consent form. Included were adult patients with a radiographically confirmed AP in a single tooth with a favorable periodontal prognosis and adequate coronal restoration, with no previous RCT. Excluded patients were those diagnosed with a systemic disease or on medications affecting bone metabolism, former and occasional smokers, pregnant patients, and those who refused to participate. Smokers were defined as those who consumed at least 100 cigarettes in their lifetime and currently smoke. Smoking intensity was classified according to cigarette consumption per day (CPD) into: heavy smoking (≥20 CPD) and mild smoking (˂20 CPD). Tobacco exposure over time was assessed by smoking index (=CPD ˟ duration of tobacco smoking in years) and categorized into: nonsmoker, <400, 400-799, and ≥800. The control group included healthy nonsmokers and matched the smoker group in termsof age and gender. All RCTs were performed by endodontic specialists following a standardized protocol. Clinical examination involved percussion and palpation tests, periodontal probing and examination of the coronal restoration; while the periapical healing was radiographically assessed using the periapical index (PAI) scoring. A total of 110 patients (55 smokers and 55 nonsmokers) were included. The two groups were comparable regarding age, gender, tooth type, socioeconomics, and periapical index scores at the baseline. The mean CPD among smokers was 12.22, and most of them were "mild smokers". At 12-month follow-up, nonsmokers showed a significantly higher healing rate compared to smokers (90.9% vs. 58.2%; χ2 = 13.846; p < 0.001). Conversely, smokers had significantly higher PAI when compared to the control group (p = 0.024). Regression analysis demonstrated that the risk of AP persistence increases with an increase in the smoking index [OR = 7.66; 95% CI: 2.51-23.28; p < 0.001, for smoking index <400 and (OR = 9.65; 95% CI: 1.45-64.14; p = 0.019, for smoking index 400-799]. Smoking was significantly associated with delayed AP healing after RCT. The likelihood of AP persistence rises as smoking exposure increases. These results could impact clinical decisions and guidelines concerning smokers.