Aim To investigate gingival inflammation and prevalence of four specific periodontal associated pathogens in Juvenile idiopathic arthritis (JIA) in relation to orofacial pain, jaw function and systemic inflammatory activity in JIA. Method Forty-five children with JIA and 16 healthy children as controls, were enrolled. Subjects were examined and classified according to the diagnostic criteria for temporomandibular disorders (DC/TMD). Pain, pain-related disability and jaw function were also assessed. A clinical periodontal examination was performed. Subgingival plaque samples were collected and analyzed for semiquantitative levels of the following periodontal pathogens; Aggregatibacter actinomycetemcomintans, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola. Results No significant difference between JIA and healthy individuals was observed regarding the clinical periodontal variables plaque, gingivitis, probing pocket depth or the investigated periodontal pathogens. P. gingivalis and T. forsythia were detected in both groups. In the group with JIA, no significant correlation was found between orofacial pain, jaw function, systemic inflammatory activity and periodontal disease, including levels of P. gingivalis and T. forsythia. Conclusions This study suggests that the periodontal diseaseassociated bacteria P. gingivalis and T. forsythia do not contribute to neither periodontal disease, systemic inflammatory activity nor orofacial pain and jaw dysfunction, including TMJ arthritis, in JIA patients in Sweden.