To detect Mycobacterium tuberculosis in clinical samples, we used the M. tuberculosis–complex specific insertion sequence IS 990 as the target in a simple DIG-PCR ELISA assay, as this element is present as a single copy in all strains of M. tuberculosis we have examined to date. The IS 990 test was compared with a similar PCR that utilizes IS 6110 as target. For detection of PCR product, digoxigenin-11-dUTP (DIG-dUTP) was incorporated into the product. After amplification, the PCR product was hybridized with biotinylated capture probe, which was complementary to the inner part of the amplicon. The hybrid was captured onto streptavidin-coated microtiter plate and DIG-labeled PCR product was detected using a peroxidase-conjugated antibody to DIG. We evaluated DIG-PCR ELISA for the detection ofM. tuberculosis DNA in 265 respiratory and non-respiratory specimens taken from patients with known and suspected tuberculosis disease or from controls. The sensitivity and specificity of both IS 990 -based test and IS 6110 -based test was 96.5% and 95.3% respectively, comparable to the sensitivity and specificity of the IS 6110 -based test. The results demonstrate that the IS 990 PCR ELISA test is a rapid and sensitive tool for the detection and identification of M. tuberculosis in clinical samples, and may have advantages to the more widely used IS 6110 -based tests, particularly in areas where IS 6110 -negative strains are found.