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Southern chamois (Rupicapra pyrenaica) share the habitat with domestic ungulates, and may, therefore, play a role in the epidemiology of shared agents. The objective of this study was to determine the seroprevalence for Brucella spp., Mycobacterium avium ssp. paratuberculosis (MAP), pestivirus, and Sarcoptes scabiei in Cantabrian chamois (Rupicapra pyrenaica parva) and compare these data with those of sympatric domestic goats (Capra hircus). From 2005 to 2008, blood samples were obtained from 236 adult Cantabrian chamois in two different populations, the western one and the eastern one. Seroprevalence for Brucella spp. and pestivirus was assessed using commercial ELISA kits, whereas specifically designed ELISA tests were used for MAP and S. scabiei. No antibodies against Brucella spp. were detected. Conversely, antibodies against MAP, pestivirus (chamois 3.8%; goat 2.3%), and S. scabiei (chamois 11.9%; goat 12.8%) were detected in both species. Seroprevalence for MAP was significantly higher for domestic goats (26%) than for chamois (9.7%). In chamois, seroprevalence for pestivirus was higher in the west (6.5%) than in the east (range 0-1.8%), whereas seroprevalence for S. scabiei followed the opposite trend (west 4.6%; east 16.7-21.4%). We suggest that certain diseases could circulate between Cantabrian chamois and domestic goat populations, and domestic livestock may suppose a threat for the health status of sympatric Cantabrian chamois.