BACKGROUND Echinococcus multilocularis, the causative agent of alveolar echinococcosis, is a fox tapeworm widely distributed in Europe with an increase of endemic area in recent years. Many mammal species including humans and non-human primates can be infected by accidental ingestion of eggs. METHODS In March 2011, a 5-year-old zoo-raised male cynomolgus macaque (Macaca fascicularis) presented a paresis of the lower limbs which evolved into paralysis. Lesions in liver and vertebra were observed on tomography scan. E. multilocularis infection was diagnosed post-mortem by morphological and histological examination and detection of Em DNA by polymerase chain reaction. Serodiagnosis of other primates of the colony using enzyme-linked immunosorbent assay (ELISA) was negative. In June 2013, at necroscopy, a hepatic and a paravertebral masses were detected in a second cynomolgus macaque of the same colony. Serology and DNA isolated from hepatic and abdominal cysts confirmed E. multilocularis infection. CONCLUSIONS We described hear vertebral and liver localization of alveolar echinococcosis in non-human primates. The animals lived in an indoor/outdoor housing facility, where the probable mode of contamination is by ingestion of food foraging around the enclosure which could be contaminated with fox feces. Serological survey in the facility should allow us to estimate the risk of human contamination and the zoonotic risk of monkey infection due to environmental contamination.