Analysis of 247 faecal enterococcal isolates from 99 healthy Portuguese individuals during 2001 revealed the presence of enterococci resistant to vancomycin (5%) and highly resistant to streptomycin (52%), kanamycin (40%) or gentamicin (11%). Most isolates were also resistant to tetracycline, erythromycin, ciprofloxacin and quinupristin-dalfopristin. The vanA (two Tn1546 types), vanC1, erm(B), aac(6')-aph(2'')-Ia, aph(3')-IIIa, vat(E) and vat(D) genes were detected. Enterococcus faecalis and Enterococcus faecium isolates with high-level resistance to gentamicin were related to Portuguese poultry isolates described previously. E. faecium isolates that were highly resistant to vancomycin or gentamicin harboured different housekeeping purK alleles associated previously with different hosts.