Brazil has the fourth largest herd of horses in the world, with more than five million animals. Disease caused by Rhodococcus equi is rare in adult horses, although cases of pleuropneumonia, enteric disease, abortion and placentitis were occasionally reported. R. equi strains are classified as virulent (vapA positive), intermediately virulent (vapB positive), and avirulent (vapA and vapB negative). The aims of this study are to describe the prevalence of R. equi in the upper respiratory tract (URT) of apparently healthy horses and its virulence profile and to evaluate epidemiological risk factors. A cross-sectional survey was performed in the state of Rio Grande do Sul and swab samples from the nasal cavities of healthy adult horses (n=1,013) were collected for bacteriological analysis. PCR targeting genus/species of R. equi and virulence genes, vapA and vapB, was performed in order to identify and classify bacterial colonies presenting R. equi profile. We analyzed risk factors considering the animal and the farm as a study unit. A prevalence of 0.99% of animals positive for R. equi in the URT was detected. These animals were distributed into 2.93% (10/341) of the proprieties. Only one isolate of R. equi was vapA positive, and none was vapB positive. Regarding the farm results, only the total number of equines (P=0.01) showed effect on the risk for R. equi isolation (RR=1.01; 95% CI, 1.00 to 1.02). In contrast, at animal level none of the factors analyzed were significant. The role of R. equi in causing a particular infection is often related to animal management than by its characteristics as virulence factors. We reinforce that R. equi (virulent and avirulent strains) reside in the URT of healthy adult horses and can cause opportunistic infections in these animals besides to be a source of infection for susceptible horses.