Objective To identify the endemic areas and endemic situation of echinococcosis in China. Methods Nine provinces and autonomous regions(Inner Mongolia, Sichuan, Tibet, Gansu, Qinghai, Ningxia, Yunnan, Shaanxi and Xinjiang (including Xinjiang Production and Construction Corps) were involved in this study during 2012-2016. In counties (cities) with suspected local cases of hydatidosis and suitable conditions for disease transmission, the numbers of administrative villages of pastoral area, semi-agricultural and semi-pastoral area, agricultural area, and town were determined according to their population sizes relative to the whole population size in the county. Sixteen villages were randomly selected, from each of which 200 residents aged > 1 year were examined by ultrasonography, accompanied by serological test for the suspected. In each county (city) surveyed, one primary school was selected from a township that was dominated by the pastoral area, semi-agricultural and semi-pastoral area, agricultural area, and town, respectively. Students in the schools were examined by ultrasonography, and blood taken for serum to detect antibody by ELISA. Twenty households raising dogs were selected from each village, and Echinococcus antigen in dog feces was detected by ELISA for one dog in each household. In each county (city), 1 000 sheep/pigs or 500 cattle raised locally were selected to examine hydatid infection in internal organs. Rodents were captured around the residence of patients with alveolar echinococcosis (AE), visceral biopsy was performed to examine lesions caused by Echinococcus multilocularis and identified by microscope. Two counties were selected In Henan and Jiangsu Provinces, respectively, where indigenous cases of hydatidosis were reported since 2000, a survey was made in human population and livestock. Then counties prevalent with echinococcosis were determined based on the survey results, local conditions for transmission, number of indigenous cases, and the prevalence of hydatidosis in regions nearby. According to the method of stratified weighting, the prevalence and the number of patients were estimated. Results A total of 413 counties were surveyed, of which 368 counties were identified as endemic counties of echinococcosis, distributed in the nine provinces and autonomous regions above. Of which, 115 counties showed mixed prevalence of cystic echinococcosis (CE) and AE. No county showed AE prevalence alone. Among 364 endemic counties, 1 001 173 residents were examined by ultrosound, of whom 5 133 (0.51%) were detected with hydatidosis, comprising 4 018 CE cases (78.28%), 1 008 AE cases (19.64%), 47 cases of mixed CE and AE (0.92%), and 60 unclassified cases (1.17%). The prevalence was estimated to be 0.28% in the whole endemic area, and the number of patients was estimated to be 166 098. Of the 364 endemic counties, 158 (43.41%) were located in Qinghai-Tibetan plateau, with a prevalence of 1.28% (4 260/332 884), higher than that of non-Qinghai-Tibetan plateau areas (0.13%, 873/668 289) (χ2 = 5 752.13, P < 0.05). The prevalence was highest in Tibet Autonomous Region (1.71%, 1 371/80 384), with significant difference comparing with other provinces (autonomous regions) (χ2 = 2 435.70, P < 0.05). The prevalence of hydatidosis in pastoral area, semi-pastoral and semi-agricultural area, agricultural area and town were 1.62% (2 901/178 544), 0.50% (1 097/219 829), 0.19% (830/435 672) and 0.21% (280/131 745), respectively (χ2 = 5 278.60, P < 0.05). The prevalence was higher in males (0.43%, 2 047/476 601) than in females (0.59%, 3 086/524 522) (χ2 = 123.27, P < 0.05). The prevalence increased with age (χ2trend = 247.99, P < 0.05), being highest in those of ≥ 90 years (1.35%, 6/443). There was a significant difference in prevalence among different occupations (χ2 = 6 138.90, P < 0.05), with highest prevalence in the religious (4.42%, 79/1 786). As to the education level, the prevalence was highest in the illiterates (1.22%, 2 968/242 423) and there was a significant difference among education levels (χ2 = 3 381.40, P < 0.05). A total of 385 878 children were examined by ultrasonography, and the prevalence was 0.10% (371/385 878). ELISA was performed in 364 770 blood samples, with an antibody positive rate of 3.03% (11 035/364 770). The positive rate was highest among children in Qinghai (5.92%, 2 693/45 507), with significant difference comparing with other provinces (autonomous regions) (χ2 = 1 481.80, P < 0.05). A total of 111 832 samples of dog feces were collected, and 4 750 were positive for Echinococcus antigen, with a positive rate of 4.25%. The positive rate of Echinococcus antigen was highest in Qinghai Province (13.02%, 1 505/11 563), with significant difference comparing with other provinces (autonomous regions) (χ2 = 2 435.50, P < 0.05). Investigation of hydatid infection in livestock (sheep, cattle and pigs) in 342 endemic counties showed a prevalence of 4.68% (10 186/217 774), among which the infection rate in livestock was highest in Tibet Autonomous Region (13.21%, 283/2 143), with significant difference comparing with other provinces (autonomous regions) (χ2 = 351.14, P < 0.05). The prevalence in sheep was 4.84% (8 448/178 946). A total of 42 734 rodents were captured in 54 counties with endemic AE, and 667 (1.56%) rodents were detected with AE. The AE prevalence was highest in the Tibet Autonomous Region (7 counties) (10.34%, 12/116), with significant difference comparing with other provinces (autonomous regions) (χ2 = 52.82, P < 0.05). In Henan Province (Jiyuan City and Xuchang City), ELISA was performed on 549 blood samples (including 49 blood samples from adults), and all showed negative. Among 474 blood samples tested by ELISA in Jiangsu Province (Liyang City and Yixing City), the positive rate of anti-Echinococcus antibody was 5.91% (28/474), and those sero-positives all showed negative results in ultralsonography. Conclusions Combining the results of this survey and previous data, there are 368 endemic counties of echinococcosis in the 9 provinces (autonomous regions), of which 115 counties showed a mixed prevalence of CE and AE. The prevalence of hydatidosis in populations is higher in Tibet, Qinghai and Sichuan, and the prevalence in livestock was higher in Tibet, Qinghai and Xinjiang. And the positive rate of echinococcus antigen in dog feces was higher in Qinghai, Tibet and Gansu.