Polymerase chain reaction (PCR) assays are useful tools for pathogen surveillance, but they are only proxy indications of pathogen presence in that they detect a DNA sequence. To be useful for detection of actual infections, PCR assays must be thoroughly tested for sensitivity and specificity, and ultimately validated against a technique, typically histology, which allows visualization of the parasite in host tissues. There is growing use of PCR assays for pathogen surveillance, but too often the assumption is made that a positive PCR result verifies an infection in a tested host. This assumption is valid only if the assay has been properly validated for the geographic area and for the hosts examined. Researchers should interpret unvalidated PCR assay results with caution, and editors and reviewers should insist that robust validations support all assertions that PCR results confirm infections.KEY WORDS: PCR assay · Validation · Histology · In situ hybridization · Marteilia · Haplosporidium Resale or republication not permitted without written consent of the publisher Dis Aquat Org 80: [81][82][83] 2008 agent in a host' to 'the presence of a multiplying or otherwise developing or latent disease agent in a host' (OIE 2007, p. 9). PCR assays alone cannot determine that a parasite has become established in a host. To be interpreted appropriately, PCR-based analyses for determination of protistan pathogen infections must be validated against an established technique, typically histology, which allows visualization of the infective agent.As defined by Hiney (2001), validation is an investigation of the extent to which a technique can be legitimately used for a particular purpose. Validation determines whether the technique detects the species, whether it detects all strains and life history stages of that species (inclusivity), and whether there is a crossreaction with any non-target species (exclusivity) (Reece & Burreson 2004). The latter is particularly problematic because it is impossible to test any assay against all other organisms, so false positives from unknown cross-reactions are always a possibility. This becomes especially important if an assay is used in a new host, or new geographic area for which it has not been validated. Sequencing of amplification products can verify that the DNA is from the target organism, but it does not confirm that there is an actual infection.Validation against histology determines the extent to which the PCR assay detects an actual infection. Validation should be accomplished by field trials in which the same sample is tested by both PCR-based methods and histology. When using PCR assays to detect parasites in hosts or geographic regions where validation of the assay has not been accomplished, infections must be verified by histology. Of course, it is well documented through many validation studies that molecular diagnostic techniques are more sensitive than histology when infections are of low intensity, especially if the parasite is small. In these circumstance...