South Tyrol has implemented, in 2007, a mandatory eradication program against Caprine Arthritis Encephalitis Virus (CAEV), a virus known to cause economic losses related to decreases in milk production and milk quality in goats, along with poor animal welfare and premature death. After a great initial decrease in the seroprevalence, the program has reached a tailing phase with scattered positivities. Potential risk factors associated with the multispecies farming system, a traditional approach in South Tyrol, are evaluated in this study, in order to better understand some of the potential causes leading to the tailing phenomenon. A statistically significant number of farms was selected for the present study, based on the risk factors evaluated. Even though there is no statistically significant association between the practices evaluated and the incidence of infection, the authors believe that it is important to highlight potential risks that may threaten the outcome of this eradication program.