Hydropericardium hepatitis syndrome（HHS）is a novel infectious disease，causing huge economic losses in the poultry industry. In this paper，with Taqman real-time PCR method，the relative virus concentrations in different tissue samples of a natural case dead chickens were measured. The results showed that the average concentration of virus in different tissues in order from high to low were：liver> lung > spleen > kidney > intestine > trachea > thymus > heart > brain > cardiac fluid > pancreas > throat /anal swab. The virus concentration among different tissues varied greatly，in which the liver virus concentration was the highest，higher than the other tissues of about 1 to 4 in the order of 10 magnitude. So liver can be used as the preferred target tissue of diagnosis，monitoring and vaccine preparation. The virus concentration of heart cytosol was not high，only 0.22% of the livers. Swab samples of virus were the lowest. It was suggested that if the swab samples were monitored，the probability of missed detection was greater，and it was necessary to increase the number of samples and other methods to make up for the lack of sample sensitivity. This paper provides a basis for the monitoring，diagnosis and research of the disease.