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Objectives: The Aptima and Cervista tests (Hologic/ Gen-Probe, San Diego, CA) were compared for detection of high-risk human papillomaviruses (HPV) in cervical cytology specimens. Methods: A total of 208 specimens were tested with both tests, and those with discordant results were tested with the Cobas HPV test (Roche Diagnostics, Indianapolis, IN). HPV test results were correlated with cytologic findings for all specimens and concurrent cervical biopsy specimens in 31 women. Results: The agreement between the results of the two tests was only 88% (McNemar test, P < .001). HPV was detected by both tests in 83 specimens, by Aptima alone in two, and by Cervista alone in 23. Both tests were negative in 100 specimens. One (50%) of two specimens positive by Aptima alone and only five (22%) of 23 specimens positive by Cervista alone were positive by the Cobas test. Of the 23 Cervista-positive/Aptima-negative specimens, 13 were positive in all three of the Cervista reaction mixtures for HPV clades A5/A6, A7, and A9, and 85% of these had high human genomic DNA fold-over-zero ratios (≥15). Conclusions: We found poor positive percent agreement between the results of the Aptima and Cervista HPV tests and described an important source of false-positive Cervista results. [ABSTRACT FROM AUTHOR]