Juvenile idiopathic arthritis (JIA) can severely disturb facial growth and affect occlusal development. In this case-control study, facial, functional, and occlusal characteristics of 100 JIA patients (35 males and 65 females; age range: 1.7-19.4 years) comprising all subtypes classified according to the revised classification criteria of the International League of Associations for Rheumatology (ILAR) were studied. They were compared with a mixed orthodontic control group (n=32; 12 males and 20 females) and with a Class II division 1 malocclusion group (n=19; eight males and 11 females). The JIA patients and controls were evaluated using clinical assessment, dental pantomograms, lateral cephalograms (LCGs), and dental casts. Compared with the age- and gender-matched mixed orthodontic controls, JIA patients showed a significantly greater prevalence of anterior open bites (AOBs; P<0.05; Wilcoxon matched pairs test). Cephalometrically, a larger mandibular plane (P<0.05) and SNA (P<0.001) angles and a smaller interincisal angle (P<0.001) were found. In comparison with the Class II division 1 controls, JIA patients showed a larger SNA (P<0.001; Wilcoxon matched pairs test) and SNB (P<0.05) angles and smaller lower anterior face heights (LAFHs; P<0.05). No differences were found for the mandibular plane, the gonial and the interincisal angles, or total face height. From this case-control study, it can be concluded that although JIA patients share occlusal characteristics with non-JIA patients with a Class II division 1 malocclusion, they are different with regard to the prevalence of condylar lesions and AOBs, as well as SNA and SNB angles and LAFH.