To determine the impact of farming over vicuña population in Peru, serum samples were collected from 207 vicuñas (126 captive vicuñas and 81 free-ranging vicuñas) and 614 domestic South American camelids (571 alpacas and 43 llamas), in ten Andean communities at the Salinas y Aguada Blanca reserve, province of Arequipa, southern Peru. Samples were tested for the presence of leptospirosis, foot and mouth disease (FMD), bovine viral diarrhea (BVD), bovine herpesvirus type 1 (BHV-1), brucellosis, bluetongue disease (BT), paratuberculosis, and neosporosis. Serological results showed that 1.9 % (4/207) of vicuñas, 18.6 % (106/571) of alpacas, and 23.3 % (10/43) of llamas were positive to one or more Leptospira serovars. One percent of vicuñas (2/207) and 2.4 % of domestic camelids (15/614) had Neospora caninum antibodies tested by ELISA, but only two vicuñas and two alpacas were confirmed by Western blot. Epidemiological evaluation found an association of leptospirosis to sex and age (p < 0.001), with female subjects older than 2.5 years at higher risk of infection. Interestingly, antibodies against Leptospira serovars were only found in captive vicuñas. This is the first study where health status of free-ranging and captive vicuñas has been compared. Results indicate minimal to nil presence of FMD, BVD, BHV-1, brucellosis, BT, paratuberculosis, and neosporosis allied to health disorders in our sample. The detection of seropositive animals against Leptospira, however, unveils the likely significance of leptospirosis in wild and domestic South American camelids, the impact of mixed husbandry over vicuña population and the risk to human health. © 2014 Springer Science+Business Media Dordrecht.