An important variable in the epidemiology of arthropodborne diseases is the intensity of transmission, which is a function of host-vector contact and the prevalence of infection in the vector population. This latter value is often difficult to estimate. It is possible to envision the application of polymerase chain reaction (PCR) assays to this problem. To accomplish this, the assay must detect a single infected vector in a pool containing a large number of uninfected individuals. It must also be possible to calculate the prevalence of infection from the number of positive pools. A PCR assay for detecting Onchocerca volvulus in pools of vector black flies is described, and an algorithm is presented to calculate the prevalence of infection in the vector population, based upon the proportion of PCR-positive pools. This algorithm should be applicable to any disease for which a PCR assay is available.