Abstract This study investigated the presence of generic and verotoxin-producing E. coli as well as enumerated faecal coliforms in 30 beef carcasses in different parts of the slaughter process (after skinning, washing and cooling) at each of three slaughterhouses of the state of Mato Grosso do Sul, Brazil. Among the total number of carcasses examined (n = 90), 39 (43.3%) had generic E. coli. Among the 270 samples analysed, 25 (9.3%) were positive after skinning, 14 (5.2%) were positive after washing and nine (3.3%) were positive after cooling. The majority of isolates of E. coli was collected from samples after skinning, which is considered a critical point of the microbial contamination of carcasses. However, the highest concentration of faecal coliforms was found after the washing step. The cooling step proved to be important to reducing the amount of hygiene-indicator microorganisms. The E. coli isolates had no stx1 or stx2 genes associated with virulence.