Antibodies to DNA (anti-DNA) play an important role in the pathogenesis of systemic lupus erythematosus (SLE). In blood, these antibodies may exist in a free, unbound state or as part of complexes with DNA. Furthermore, circulating DNA may be either complexed or free. Because of the central role of these immunoreactants (anti-DNA and DNA) in the disease, monitoring of their levels could provide valuable information for both clinical and investigative purposes. In these studies, we have explored the use of a DNA-binding dye, PicoGreen, for the detection of circulating DNA, either total or immune complex bound. In addition, we have used this dye for Farr-type antibody assays. Using autoimmune MRL/lpr mice as a model, we have shown that, while the levels of free DNA in the plasma of these mice were comparable with those of normal BALB/c mice, the amounts in complexes precipitable by ammonium sulfate were significantly greater. Furthermore, we showed that Farr assays using PicoGreen reliably detect levels of free anti-DNA, with values correlated with anti-DNA levels by an enzyme-linked immunosorbent assay. Together, our results suggest that a fluorometric dye can accurately monitor DNA and anti-DNA antibody levels in SLE and may provide important information on immunopathogenesis.