Pathological studies of iliocecal valve, ileum and jejunum from forty two goats randomly selected from two paratuberculosis infected flocks were performed. In twenty nine goats, lesion of paratuberculosis were observed. Ten of them had lesions in the Peyer's patches only. Cultures from the same samples were made in Lowenstein-Jensen medium without piruvate and positive results were obtained in twenty one animals, all of them with paratuberculosis lesions. With serum samples, the AGID and ELISA techniques were applied by using PPA-3 antigen. The AGID test had 55.1% sensitivity and 84.6% specificity; ELISA had 65.5%, 84.0% sensititivty and specificity, respectively, using the pathological results as a reference. The ELISA test detected 100% of the animals with severe lesions, 64% with less important lesions and 50% with lesions located in Peyer's patches only. The high prevalence of infection (69%) in paratuberculosis flocks of goats, with poor sensitivity of serological diagnosis tests, which detected animals with severe lesions, must be addressed.