Faecal samples of 270 dogs and 100 cats from 3 animal shelters in Germany were comparatively examined using conventional coproscopical methods and commercial coproantigen ELISA kits for the detection of Giardia and Cryptosporidium infections. Giardia cysts were found in 9.5% and 0% of the faecal samples in dogs and cats, respectively, examined once using the ZnCl2-NaCl flotation. However, the Giardia coproantigen ELISA (ProSpecT(R) Giardia Microplate Assay) was positive in 29.5% and 22.4% of the samples from dogs and cats, respectively. Direct faecal smears stained with carbol fuchsin showed Cryptosporidium oocysts in one dog (0.4%) and one cat (1%). In contrast, the Cryptosporidium coproantigen ELISA (ProSpecT(R) Cryptosporidium Microplate Assay) reacted positively in 23% of the samples from dogs and 30% of the samples from cats. Both coproantigen ELISAs were more often positive in coproscopically Giordia-negative canine faecal samples that contained Isospora burrowsi/ohioensis oocysts than in faecal samples without any parasite stage. Possible reasons for these observations are discussed.