Direct PCR detection of bacteria in clinical samples is often hindered by the presence of compounds that inhibit the PCR. To improve and accelerate the diagnosis of Mycobacterium avium-M. intracellulare complex infection, an immunomagnetic PCR (IM-PCR) assay was developed. This IM-PCR procedure combines the separation of mycobacteria by antimycobacterial monoclonal antibody coupled to magnetic beads with an M. avium-M.intracellulare complex-specific PCR protocol based on 16S rRNA gene sequences. In this protocol, the inclusion of an internal control also facilitates efficient assessment of the PCR results. As few as 10 M. avium bacilli were detected in spiked human stool samples, a clinical specimen usually refractory to conventional PCR analysis, by the IM-PCR method. Moreover, M. avium organisms were detected in about 24 h in 18 of 22 culture-confirmed fecal samples from AIDS patients. This IM-PCR protocol should allow for the rapid and sensitive detection of M. avium isolates in clinical specimens.