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<p>Abstract</p> <p>Background</p> <p>Clonorchiasis, caused by <it>Clonorchis sinensis</it>, is one of the major parasitic zoonoses in China, particularly in China's southern Guangdong province where the prevalence of <it>C. sinensis </it>infection in humans is high. However, little is known of the prevalence of <it>C. sinensis </it>infection in its reservoir hosts dogs and cats. Hence, the prevalence of <it>C. sinensis </it>infection in dogs and cats was investigated in Guangdong province, China between October 2006 and March 2008.</p> <p>Results</p> <p>A total of 503 dogs and 194 cats from 13 administrative regions in Guangdong province were examined by post-mortem examination. The worms were examined, counted, and identified to species according to existing keys and descriptions. The average prevalences of <it>C. sinensis </it>infection in dogs and cats were 20.5% and 41.8%, respectively. The infection intensities in dogs were usually light, but in cats the infection intensities were more serious. The prevalences were higher in some of the cities located in the Pearl River Delta region which is the most important endemic area in Guangdong province, but the prevalences were relatively lower in seaside cities.</p> <p>Conclusions</p> <p>The present investigation revealed a high prevalence of <it>C. sinensis </it>infection in its reservoir hosts dogs and cats in China's subtropical Guangdong province, which provides relevant "base-line" data for conducting control strategies and measures against clonorchiasis in this region.</p>