Objective To make an investigation on echinococcosis among animals in Gannan Tibetan Autonomous Prefecture. Methods 21 villages from Maqu and Luqu counties were selected for the survey in August of 2004-September of 2007. Rodents were trapped in the field. Sheep and yak livers, hearts and lungs were collected from the local slaughterhouses for pathological examination. Domestic dogs (shepherd dogs) were de-wormed by 15% arecoline to receive adult worms and stray dogs were shot for dissection. Results The prevalence of alveolar echinococcosis (AE) in Ochotona daurica was 1.2%(1/87), and 2.3% (3/132) in Myospalax fontanieri, but no infection was found in Marmota himalayana, Ochotona tibetana and Mus musculus. 113 out of 1 021 (11.1%) sheep were found infected with cystic echinococcosis (CE), and 3 (0.3%) with AE. 126 out of 634 (19.9%) yaks were infected with CE, and 2 yaks (0.3%) with AE. 17 out of 74 (23.0%) dogs were infected with Echinococcus granulosus (Eg), and 4 (5.4%) with Echinococcus multilocularis (Em). Conclusion The results showed that there is a widespread endemic of Echinococcus granulosus in dogs and wild animals in Gannan Tibetan Autonomous Prefecture, with less Echinococcus multilocularis infection.