Objective: To investigate changes in the craniofacial skeleton in relation to the changes in condylar alterations that occur during long-term follow-up in patients with juvenile idiopathic arthritis. Materials and Methods: Temporomandibular joint (TMJ) involvement is defined as a condylar alteration that is observed on the orthopantomogram. Lateral cephalograms were used to determine linear and angular measurements. Results: Seventy of 97 patients from the initial study cohort were included, with a mean followup of 68 months. The overall prevalence of condylar alterations and posterior rotation of the mandible decreased; however, the prevalence of retrognathia remained the same. Patients showed improvement in the degree of retrognathia and posterior rotation (40% ANB, 51% OP-SN, and 44% GO-GN-SN). Improvement in the degree of retrognathia was seen more often in patients with improved condylar alterations than in patients with persistent alterations and in those without alterations (50%, 33%, and 28%, respectively). The degree of posterior rotation improved almost equally in patients without TMJ involvement and in patients with improved condylar alterations (57% and 50% by OP-SN, and 67% and 38% GO-GN-SN, respectively) and did not improve in patients with stable persistent alterations. Conclusion: Both condylar and craniofacial alterations can improve in patients with juvenile idiopathic arthritis.