Faecal samples from 15 foxes experimentally infected with Echinococcus multilocularis were examined until 90 days post-infection (dpi) by microscopical identification of eggs isolated by flotation/sieving, by coproantigen-enzyme-linked immunosorbent assay (cELISA), by polymerase chain reaction (PCR) on DNA, respectively, isolated directly from the faecal samples (copro-DNA PCR) and from the eggs obtained by the flotation/sieving procedure (egg-DNA PCR). Based on egg counts, three periods of the infection were defined: pre-patent (2–29 dpi), high patent (30–70 dpi) and low patent periods (71–90 dpi). Whereas all methods were highly sensitive with samples from the high patent period, cELISA was the most sensitive to detect pre-patent infections (63%). Samples from the low patent infections were positive in 77% by microscopy and in 80% by egg-DNA PCR, being significantly more sensitive than cELISA and copro-DNA PCR. The isolation of eggs from the faecal material proved to be more sensitive by the flotation/sieving procedure as compared to the classical concentration McMaster technique.