Anthelmintic (praziquantel) baiting of wild red foxes against Echinococcus multilocularis infection was studied in a highly epizootic suburban area of Otaru, Hokkaido (the northern island of Japan) during the summer and autumn in the years 1999-2004. Acceptance of baits containing the biomarker tetracycline (TC) was evaluated. The prevalence of E. multilocularis infection in foxes before baiting (1999-2000) was 58% (88/153), whereas in the fourth year of bait distribution year (2004), it decreased to 11% (5/45). Analysis of TC marking in the teeth of foxes showed that 39% (77/195) of those captured after baiting were estimated to have consumed baits in the year of capture. Importantly, more juvenile (56%, 49/87) than adult foxes (26%, 28/108) were marked, indicating efficient baiting of juveniles, which tended to have a higher worm burden of E. multilocularis. Of 77 marked foxes, E. multilocularis and Alaria alata (monitored as the second indicator species of deworming) were not detected in 70 (90%) and 76 (99%) foxes, respectively. The results suggest effective deworming by bait consumption. However, it was also demonstrated that 9% of the marked foxes were infected or re-infected after bait consumption, suggesting high infection pressure and the importance of frequent baiting.