Antigen DNA isolated from immune complexes present in plasma of three patients with active systemic lupus erythematosus using an affinity column was cloned and sequenced. One clone, designated pKS7, was found to have a region homologous with that of the E. coli metK gene, and another, designated pKS8, had a region homologous with a sequence including the replication origin of bacteriophage f1. Gel retardation assay revealed that pKS7 and pKS8 interacted with the patient's IgG fraction to form immune complexes, respectively. The affinity-purified antigen DNA was proved to be originated from bacteria or bacteriophage.