The present study is the first comprehensive analysis of human cystic echinococcosis (CE) epidemiological data carried out in the province of Neuquén, Patagonia Argentina, after 34 years of uninterrupted control program. A retrospective study of all the official records of confirmed human CE cases between 1995 and 2004 was carried out. A total of 1107 cases were reported. The overall mean annual incidence (MAI) was 24.4 per 100,000 inhabitants for the total population and 9.7/100,000 in the 0-14 year group. Distribution of cases by age and sex as well as frequency of cyst locations was analysed. Children accounted for 13.3% of total cases, indicating active transmission of the disease. Territorial distribution of cases was highly heterogeneous: MAI per 100,000 ranged from 7.9 in the Metropolitan Sanitary Area to 78.4 in the western rural areas. Higher values were recorded in small communities as Pilo Lil (800/100,000). MAI showed a significant decrease from 1995 to 1999 (43.9-18.8) but remains stable from 2000 to 2004 (15.9-15.5). These results suggest that standard control measures, despite long-term implementation, are not able to produce a sustained improvement of the epidemiological status of the disease. Further studies about local transmission cycles, definite and intermediate hosts present, Echinococcus granulosus strains or cultural behaviours in small communities are required in order to adequate the control actions in Neuquén.