| Summary: | <i>Neospora caninum</i>, <i>Toxoplasma gondii</i>, <i>Cryptosporidium</i> and <i>Eimeria</i> cause severe impacts on the productivity of goat herds. The objectives of the present study were to establish the prevalence of these apicomplexans in goat farms from Ecuador; to evaluate a rapid test for <i>Cryptosporidium</i> diagnosis and to identify the risk factors associated with the infections. A questionnaire was designed to obtain information from 24 goat farms from Zapotillo, Garza Real, Cazaderos, Limones and Paletillas parishes in Ecuador. Blood (<i>n</i> = 388) and feces (<i>n =</i> 391) samples were collected. Indirect ELISA and standard parasitological assays were carried out to evaluate the seroprevalence of <i>N. caninum</i> and <i>T. gondii</i> and to detect oocysts of <i>Cryptosporidium</i> and <i>Eimeria</i>. The overall prevalence values of <i>N. caninum</i> and <i>T. gondii</i> were 12.11% and 18.20%, <i>Cryptosporidium</i> spp. and <i>Eimeria</i> spp. oocysts were detected in 10.49% and 89.51% of the total samples. A low correlation value was found between the results obtained by Ziehl-Nielsen and the rapid test. The multinomial logistic regression analysis revealed that vitamin supplementation, age of diarrhea, frequency of deworming, pasture area, presence of artiodactyls, domestic fowl, administration of sulfas, age group, body condition, abortions, type of pastures and the presence of cattle were risk factors according to the parasite species.
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