dAmoebic keratitis (AK) is a potentially blinding infection, the prompt diagnosis of which is essential for limiting ocular morbidity. We undertook a quality improvement initiative with respect to the molecular detection of acanthamoebae in our laboratory because of an unusual case of discordance. Nine ATCC strains of Acanthamoeba and 40 delinked, biobanked, surplus corneal scraping specimens were analyzed for the presence of acanthamoebae with four separate real-time PCR assays. The assay used by the Free-Living and Intestinal Amebas Laboratory of the CDC was considered the reference standard, and the performance characteristics of each individual assay and pairs of assays were calculated. Outcome measures were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Of 49 included specimens, 14 (28.6%) were positive by the gold standard assay, and 35 (71.4%) were negative. The sensitivities of the individual assays ranged from 64.3% to 92.9%, compared to the gold standard, while the specificities ranged from 88.6% to 91.4%. The PPVs and NPVs ranged from 69.2% to 78.6% and from 86.1% to 96.9%, respectively. Combinations of assay pairs led to improved performance, with sensitivities ranging from 92.9% to 100% and specificities ranging from 97.1% to 100%. ATCC and clinical strains of Acanthamoeba that failed to be detected by certain individual assays included Acanthamoeba castellanii, Acanthamoeba culbertsoni, and Acanthamoeba lenticulata. For three clinical specimens, false negativity of the gold standard assay could not be excluded. Molecular diagnostic approaches, especially combinations of highly sensitive and specific assays, offer a reasonably performing, operator-independent, rapid strategy for the detection of acanthamoebae in clinical specimens and are likely to be more practical than either culture or direct microscopic detection.A moebic keratitis (AK) is a potentially blinding eye infection caused by the parasite Acanthamoeba, which is a ubiquitous, free-living organism found in soil and other environmental sources (1). This infection usually occurs in the context of contact lens use, and outbreaks of AK have been linked to contact lens solutions that are inefficient in killing acanthamoebae adhering to the contact lenses during washing with amebacontaminated water, including the most recent outbreak in the United States, which affected 138 people (2) and led to the recall of several contact lens solutions and products by both the FDA and Health Canada (3, 4). Delays in diagnosis have been associated frequently with poor visual outcomes and more severe clinical progression in AK (5, 6). Traditional diagnostic procedures include direct microscopic examination of corneal scrapings or contact lens fluids stained with Giemsa stain, periodic acid-Schiff stain, hematoxylin and eosin, or acridine orange and culture of specimens on nonnutrient agar overlaid with Escherichia coli or Klebsiella pneumoniae; both methods are limited by poor sensitivity, operator dependence,...