The course of enzootic pneumonia, caused by Mycoplasma hyopneumoniae, is strongly influenced by management and housing conditions. Other factors, including differences in virulence between M. hyopneumoniae strains, may also be involved. The aim of this study was to evaluate the virulence of six M. hyopneumoniae field isolates and link it to genetic differences as determined by randomly amplified polymorphic DNA (RAPD) analysis. Ninety, conventional M. hyopneumoniae-free piglets were inoculated intratracheally with the field isolates, a virulent reference strain or sterile culture medium. Animals were examined daily for the presence of disease signs and a respiratory disease score (RDS) was assessed per pig. Twenty-eight days post infection, pigs were euthanized, blood sampled and a lung lesion score was given. Lung samples were processed for histopathology, immunofluorescence testing for M. hyopneumoniae and isolation of M. hyopneumoniae. RAPD analysis was performed on all M. hyopneumoniae strains. Significant differences between isolates were found for the RDS, lung lesion score, histopathology, immunofluorescence and serology. Based on the results of the different parameters, isolates were divided into three "virulence" groups: low, moderately and highly virulent strains. Typically, a 5000 bp RAPD fragment was associated with the highly and moderately virulent strains whereas it was absent in low virulent strains. It was concluded that high variation in virulence exists between M. hyopneumoniae strains isolated from different swine herds. Further studies are required to determine whether the 5000 bp fragment obtained in the RAPD analysis can be used as a virulence marker.