Our objectives were to evaluate the oral health and the masticatory system of 48 juvenile systemic lupus erythematosus (JSLE) patients and to compare them with 48 healthy children and adolescents. Demographic data, clinical manifestations and therapies of JSLE were reviewed. The DMFT index (DMFTI), the plaque (PI) and the gingival bleeding (GI) indices, dental relationship, facial profile, clinical dysfunction and mandibular mobility indices were evaluated. The two groups were homogeneous regarding age, gender, Brazilian social-economic class and dental decay index (P > 0.05). Of note, the medians of the PI and the GI were higher in JSLE patients than in controls (61.5 versus 38.10, P = 0.003 and 26.0 versus 15.95, P = 0.014; respectively). Likewise, a linear statistical correlation was evidenced between the JSLE duration and the GI (P = 0.017, r = 0.11), cumulative dose of prednisone and the PI (P = 0.01, r = 0.385) and cumulative dose of prednisone and the GI ( P = 0.001, r = 0.471). The clinical dysfunction and mandibular mobility indices were higher in JSLE patients versus controls (P = 0.002, P = 0.025). Moreover, the median of the mandibular mobility index was higher in JSLE patients who used at least one immunosuppressive than on those who did not use this medication (P = 0.0001). These results suggest that JSLE patients had an inadequate oral hygiene, higher incidence of gingivitis and temporomandibular joint dysfunction.