The aim of this study was to establish the diagnosis and isolation of virulent variants of Rhodococcus equi strains and their association with respiratory and digestive disorders or both in Thoroughbred foals. Blood samples were collected from 86 foals ranging 1 to 6 months of age with presence of respiratory and digestive clinical signs between 2006 and 2008 in nine farms of the Metropolitan Region, Chile. All samples were processed and analysed by PCR to detect the presence of R. equi and its virulence-associated proteins (Vap) (A, C, D, E, F, H). Results showed that 41.9% of the foals were positive to R. equi. The virulence factors detected in foals with respiratory disorders were vapA, vapC and vapG in 5.8% of the sampled population, with Spearman's association values of r = 0.885; r = 0.976; r = 0.885 respectively. No virulent variants of R. equi were identified in foals with digestive disorders.