In the current study we screened Escherichia coli from intestine of pigs slaughtered in Mato Grosso, Brazil, for virulence-markers related to human disease. Furthermore, we employed for the first time a phylogenetic assay to explore the association between phylogeny and virulence genotype in E. coli from finished swine. A low prevalence (7.8%) of E. coli harbouring virulence genes was observed. Among the positive isolates, 3.3% could be classified as atypical EPEC, 2.2% as STEC and 2.2% as CDT harbouring E. coli. Virulence genes were not found to co-occur in a strain. Phylogenetic determination of isolates revealed a low prevalence of E. coli lineages related to disease. Therefore, preliminary sampling of 74 pigs indicated that slaughter swine may not be major reservoirs of E. coli capable of causing human disease. In light of the significant association between phylogeny and virulence genotype, we also underscored the phylogenetic grouping of strains as a valuable tool for E. coli surveillance programmes in slaughterhouses.