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Background: Schistosoma japonicum is a major public health concern in the Peoples' Republic of China (PRC), with about 800,000 people infected and another 50 million living in areas at risk of infection. Based on ecological, environmental, population genetic and molecular factors, schistosomiasis transmission in PRC can be categorised into four discrete ecosystems or transmission modes. It is predicted that, long-term, the Three Gorges Dam (TGD) will impact upon the transmission of schistosomiasis in the PRC, with varying degree across the four transmission modes. Methodology/Principal Findings: We undertook longitudinal surveillance from 2002 to 2006 in sentinel villages of the three transmission modes below the TGD across four provinces (Hunan, Jiangxi, Hubei and Anhui) to determine whether there was any immediate impact of the TGD on schistosomiasis transmission. Eight sentinel villages were selected to represent both province and transmission mode. The primary end point measured was human incidence. Here we present the results of this five-year longitudinal cohort study. Results showed that the incidence of human S. japonicum infection declined considerably within individual villages and overall mode over the course of the study. This is also reflected in the yearly odds ratios (adjusted) for infection risk that showed significant (P<0.01) downward trends in all modes over the follow-up period. Conclusions/Significance: The decrease in human S. japonicum incidence observed across all transmission modes in this study can probably be attributed to the annual human and bovine PZQ chemotherapy. If an increase in schistosome transmission had occurred as a result of the TGD, it would be of negligible size compared to the treatment induced decline seen here. It appears therefore that there has been virtually no immediate impact of the TGD on schistosomiasis transmission downstream of the dam. Author Summary: Schistosomiasis, caused by Schistosoma japonicum, is a significant parasitic disease and public health problem in China. How the parasite is transmitted there can be categorized into four distinct modes (modes I–IV) and it is predicted that the Three Gorges Dam, recently completed, will affect the way schistosomiasis is spread in these modes. We monitored transmission for a 5-year period (2002–2006) in eight villages, representative of the three modes (I–III) below the dam across four provinces (Hunan, Jiangxi, Hubei and Anhui) to determine whether there was any immediate impact of the dam on schistosomiasis spread. Human schistosomiasis incidence declined considerably within individual villages and each mode, and the yearly odds ratios (adjusted) for infection risk showed significant downward trends in all three modes over the follow-up period. The decreased human S. japonicum incidence recorded across transmission modes I–III was probably attributable to annual human and bovine praziquantel drug treatment. If an increase in schistosome transmission had occurred as a result of the dam, it would be of negligible size compared with this treatment-induced decline. There had thus been virtually no immediate impact of the TGD on schistosomiasis transmission downstream of the dam over the 5-year surveillance period. [ABSTRACT FROM AUTHOR]