AbstractIntroductionBacterial contamination of the temporomandibular joint (TMJ) by needle penetration of the skin has previously been discussed as a contributing factor in joint arthritis. The purpose of this study was to investigate the presence of bacterial deoxyribonucleic acid (DNA) in synovial fluid, and to detect any possible iatrogenic contamination during arthrocentesis of the TMJ in patients with juvenile idiopathic arthritis and rheumatoid arthritis.MethodSynovial fluid (SF) and skin swab samples (before and after disinfection) were collected from 54 TMJs in 30 patients with TMJ arthritis. Bacterial detection and classification was performed using 16S rRNA pyrosequencing.ResultsBacterial DNA was detected in 31 joints (57%) in 19 patients (63%). In six 12 joints (20%) in six patients specific bacterial species were detected in both skin samples and in the TMJ, indicating a possible contamination. 22 different bacterial species were detected in synovial fluid from these six patients.ConclusionBacterial DNA in TMJ SF with contamination was detected in 20% of the patients. Studies are needed to evaluate the consequences of potential contamination with bacterial DNA in SF with regard to arthrocentesis and treatment of TMJ arthritis.