HindIII cleaved human intestinal spirochete genomic DNA was cloned into the plasmid vector pBluescript. The inserts from three of these clones (pRB.C33, pRB.C47 and pRB.F11) successfully hybridized with DNA from the nine human intestinal spirochetes used in this study. The fourth insert (from clone pRB.A8) failed to hybridize with DNA from two of these isolates (HRM4 and HRM9), and, all four of the inserts hybridized with the M1 strain of swine intestinal spirochete Treponema innocens. Hybridization with DNA from the P18 strain of Treponema hyodysenteriae was observed only for the probe pRB.F11. No hybridization was detected with the human strain of Borrelia burgdorferi. With these probes we were thus able to demonstrate, in southern blot experiments, a restriction site polymorphism among the isolates of the human intestinal spirochetes we tested.