Background <p>The aim of this cross-sectional study was to analyze the cortical and trabecular bone density, as well as the cortical bone thicknesses of the mandibular condyles in subjects with Juvenile Idiopathic Arthritis (JIA) and compare them with the condyles of control subjects.</p> Materials and methods <p>Patients aged between 7 and 16 years were included in the study. A total of 75 CBCTs were analyzed, including 25 from patients with unilateral JIA (mean age 11.1 ± 2.2), 25 from patients with bilateral JIA (mean age 11.9 ± 2.6), and 25 from control subjects (mean age 11.7 ± 2.5). Mimics^® (Materialise software BV, Leuven, Belgium) was used for measurements of bone density and cortical bone thicknesses. Total (DTo), cortical (DCo), and trabecular bone density (DTr), as well as cortical bone thicknesses at the medial (MCBT), lateral (LCBT), and upper (UCBT) poles of the condyle’s head, were analyzed. The Paired t-test was used to compare the condyles within each group, and the independent t-test was performed to assess differences between the healthy condyles of unilateral JIA subjects and the controls. A three-group multiple regression model, weighted by sex, age, side, and clinic of the condyles (whether healthy or affected), was computed to perform a between-groups comparison.</p> Results <p>A statistically significant difference (<i>p</i> = 0.02) was found in DTr (-23.26 ± 48.61 HU) and UCBT (-0.35 ± 0.24&#xa0;mm) between the affected and unaffected sides in the unilateral JIA group. In bilateral JIA patients, a statistically significant difference in total bone density (<i>p</i> &lt; 0.01) and trabecular bone density (<i>p</i> &lt; 0.01) of the condylar head was noticed between the right and left sides, with significantly higher values on the right side. The multiple regression model showed a significant influence of the pathology on DTr (-23.53 ± 8.70 HU) and UCBT (-0.35 ± 0.03&#xa0;mm) of the affected condyles.</p> <p>Analyzing the differences between the control group and the Bilateral JIA subjects, it was found that there was a statistically significant reduced thickness of MCBT (0.11 mm ± 0.05), LCBT (-0.13 mm ± 0.05), and UCBT (-0.11 mm ± 0.04). The affected side of unilateral JIA subjects showed a statistically significant reduction in UCBT (-0.06 ± 0.03 mm) compared to the controls.</p> Conclusions <p>The results suggest that in affected JIA condyles, the rheumatic disease has a significant impact on the bone structures, impairing trabecular bone density and cortical bone thickness, particularly at the level of the upper pole.</p>