The findings of bacterial antigens in the joint and persistent triggering infection elsewhere in the body are thought to be important in the pathogenesis of reactive arthritis (ReA). We describe a patient with clinical and laboratory features consistent with this. The initial presentation with erythema nodosum and periarthritis due to infection with Yersinia pseudotuberculosis IV was followed 13 months later by recurrent erythema nodosum with joint effusion. At that time, synovial fluid was shown to contain Yersinia antigens, and, surprisingly, Yersinia-specific 16S ribosomal RNA (rRNA) sequences were also identified by reverse transcriptase-polymerase chain reaction and sequencing. Since there was no serologic evidence of reinfection, we postulate that a silent persistent Yersinia infection was reactivated, leading to dissemination of organisms to the joint, with consequent induction of ReA. Although the finding of synovial Yersinia antigens years after the original infection in ReA has previously been reported, the presence of Yersinia 16S rRNA indicates that viable organisms were also able to reach the joint.