The polymerase chain reaction (PCR) test is increasingly being used as the diagnostic tool of choice and with pathogens of aquatic animals, particularly molluscs and crustaceans, a PCR test is often the only laboratory diagnostic test available. When a diagnostic decision is required in the absence of clinical disease (e.g. health certification or a survey for disease freedom) limitations with the PCR technique may become apparent. A review of validated PCR tests demonstrates that most are imperfect assays with diagnostic sensitivities and/or specificities less than 100%. False positive and false negative results will thus occur and large numbers of samples need to be tested to achieve statistically significant results. The results from a survey for disease freedom from white spot syndrome virus in Australia are used to illustrate the problem and to assess various solutions. The use of pooled samples or the use of two independent PCR tests can substantially reduce the number of tests required and the associated costs of such a survey.