A polymerase chain reaction (PCR) method was developed in order to permit a sensitive and specific identification of Echinococcus multilocularis DNA from fox faecal specimens. In an attempt to overcome problems related to the presence of endogenous PCR inhibitors in faecal extracts, we investigated a DNA extraction technique using an anion binding resin (Gene-Fizz). This simple and rapid procedure was applied to 61 faecal samples. Compared with the traditional microscopic examination, the sensitivity of PCR using Gene-Fizz was 82.3% and the specificity was 95.5%. No PCR signal was obtained for 20 Echinococcus granulosus isolates, showing that this method allowed discrimination between E. multilocularis and E. granulosus. Large-scale epidemiological surveys of fox excrements may be possible by using Gene-Fizz treatment prior to PCR amplification reactions.