According to the World Health Organization (WHO 2000) more than 120 million people, worldwide, live under risk of acquiring onchocerciasis and 18 million are infected. One third of those infected manifest dermatitis and 500,000 present serious visual problems with approximately 1% developing blindness. Indeed, 270,000 individuals are blind from this etiology worldwide. This disease is caused by infection with Onchocerca volvulus (Nematoda: Onchocercidae) and is endemic to Africa, the Arabian Peninsula, and Latin America, where it occurs in parts of Brazil, Colombia, Ecuador, Guatemala, Mexico, and Venezuela. In Brazil, the only known active focus of the disease is located in the Amazonian region, and extends across the border to form the southern focus of Venezuela. It corresponds to more or less the whole territory of the Yanomami in the northwest of the state of Roraima and central north of the state of Amazonas (Shelley 1991(Shelley , 2002, exposing 13,767 indians to the infection (Funasa 2002).In the New World the control program has been sponsored by the Onchocerciasis Elimination Program for the Americas (OEPA). This program has as its main strategy the elimination of the disease through the semi-annually distribution of the ivermectin (Mectizan™) for 10 to 15 years to the population at risk (Blanks et al. 1998). This approach has been demonstrated to result in a decrease of microfilariae rates in the skin which gives immediate clinical benefit and reduces the possibility of infecting new vectors which is expected to reduce or eliminate transmission (Greene et al. 1989, Duke 1990.In simuliids, the classic parasitological method for the parasite detection (by dissection and examination of vectors) is unsuitable for high throughput analysis because it is time consuming and requires high levels of training, for example it requires the accurate morphological identification of the larvae.Since the 1990s, the polymerase chain reaction (PCR) amplification of an Onchocerca-specific repeated DNA sequence (O-150) has been used to detect and identify O. volvulus (Meredith et al. 1991, 1994, Zimmerman et al. 1992, Fischer et al. 1996, Merriweather & Unnasch 1996, Unnasch & Meredith 1996. However, in populations of vectors with a low prevalence of infection (as would be expected during an onchocerciasis control program using ivermectin, for example) large numbers of flies would have to be processed to obtain an accurate estimate of infection, which would be timeconsuming and expensive. However, the O-150 PCR has proved to have a high analytical sensitivity, being able to detect a single infected fly in pools containing up to 100 flies (Katholi et al. 1995). Therefore, a statistical model has been developed by Katholi et al. (1995) to determine the prevalence of infection in the simuliid population, based on the prevalence of infection in pools of vectors, and it has been demonstrated that this method reveals a prevalence of infected flies statistically similar to the rates obtained by traditional entomological dissect...