Atopobium vaginae, a fastidious, anaerobic, Gram-positive cocci-shaped bacterium that generates large quantities of lactic acid, is associated with bacterial vaginosis (BV). Published nucleic acid amplification tests for identifying A. vaginae are directed toward the 16S ribosomal DNA with suboptimal specificity and require isolation of the organism. Here, sequencing of an A. vaginae genomic library has led to the development of a highly specific and sensitive real-time PCR test for detection of A. vaginae directly from gynecological cervicovaginal swab samples. The real-time PCR did not cross-react with DNA extracted from other members of the Atopobium genus, species with closely related 16S ribosomal DNA, and a panel of 51 other human pathogens. The DNA extraction and PCR assembly were amenable to automation using Corbett Robotics X-tractor Gene and CAS-4200N liquid handling systems. The real-time PCR was used to analyze 96 cervicovaginal swab samples submitted to our clinical laboratory for detection of organisms associated with BV. Of those samples, 28 were positive for A. vaginae. Of the 28 positive samples, 23 were concomitant with Gardnerella vaginalis detection. These results suggest that further clinical study of the relationship of A. vaginae with G. vaginalis and the development of BV should be performed.