Pulsed field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP) were compared for their ability to differentiate between 50 porcine Serpulina pilosicoli isolates. Both techniques were highly sensitive, dividing the isolates into 36 and 38 groups, respectively. Due to the low workload and high capacity and sensitivity of AFLP, this technique is recommended for future studies of S. pilosicoli. S. pilosicoli isolates were genetically diverse, and generally, identical subtypes were only identified in cultures from the same herd. (C) 1999 Academic Press.