Echinococcus multilocularis, Toxoplasma gondii and Toxocara spp. are foodborne parasites whose eggs or oocysts are spread in the environment via canid or felid faeces. They can cause infections in humans following the raw consumption of contaminated fruit or vegetables. In this study, their occurrence was investigated by quantitative polymerase chain reaction (qPCR) in 254 carnivore faeces deposited in 94 kitchen gardens of northeastern France that were sampled between two and six times from October 2011 to April 2013. Less than 25% of the sampled kitchen gardens contained more than 75% of the collected faeces. Of the 219 faeces that could be attributed to an emitter, cat accounted for 58%, fox for 32% and dog for 10%. Echinococcus multilocularis was detected in 35%, 11% and 7% of fox, dog and cat faeces, respectively, and Toxocara spp. in 33%, 12% and 5.5% of cat, fox and dog faeces, respectively. Toxoplasma gondii was detected in 2/125 cat faeces and 2/21 dog faeces. The 34 faeces that tested positive for E. multilocularis were found in only 19 out of the 94 sampled kitchen gardens, and the 40 faeces that tested positive for Toxocara spp. were found in 28 of them. Consequently, some kitchen gardens appeared particularly at risk of human exposure to foodborne parasites, including E. multilocularis responsible for alveolar echinococcosis (AE), which is a serious zoonosis. In endemic areas, kitchen garden owners should be informed about the zoonotic risk linked to carnivore faeces deposits and encouraged to set up preventive measures.