This study aimed to determine the association between the root taper and proximity of single-rooted teeth with periodontitis using cone-beam computed tomography (CBCT). CBCT images of 362 single-rooted teeth from 37 patients were evaluated. This case-control study analyzed 17 participants with stage II and III periodontitis, (n = 161 teeth, periodontitis group) and 20 participants with healthy periodontium (n = 201 teeth, control group). Multiplanar reconstructions were used for proximity measurements, and cross-sectional images for calculating the angle of the root tapers. Root proximity, root length, and root taper were measured. Multivariate binary logistic regression analysis was used to determine association with periodontitis. In the periodontitis group, the upper lateral root-taper was 18.33 degrees +/- 3.25 degrees and was significantly higher when compared to the control group (p = 0.001). The root taper of the lateral incisor was associated with the diagnosis of periodontitis (p = 0.01) with an odds ratio of 1.541 according to regression analysis. Root length was also identified as a potential protective parameter. The risk of being diagnosed with periodontitis decreases when root length increases by 0.785 times (p = 0.043). Upper canines in the periodontitis group presented shorter root lengths (p = 0.039) and higher root tapers (p = 0.01). Also, mandibular canines were closer form adjacent teeth in the periodontitis group (p = 0.042). This study indicated that short-root and increased root-taper at specific teeth could be considered as risk indicators for periodontitis.