The purpose of the present study was to investigate the occurrence of Bacteroides forsythus in infections of dental root canals. Eleven samples from infected root canals were analyzed by four different molecular methods. The prevalence of the monitored species varied as a function of the detection method. The polymerase chain reaction-DNA probe method after immunocapture yielded the highest prevalence value (6/11), whereas the lowest value was observed with the slot-blot (3/11). Of the 11 canal samples, 5 were positive by ELISA and 4 were positive by immunofluorescence. The presence of B. forsythus was detected by all four methods in 3/11 canals, whereas 4/11 appeared to be free of B. forsythus. Our data indicate that B. forsythus can be part of the endodontic microflora. The procedure consisting of immunomagnetic capture and a polymerase chain reaction-DNA probe assay can be useful as an alternative to culture for clinical studies of the species infecting human dental pulp.