Acute outbreaks of gill hemorrhages of crucian carp () can cause high mortality rates, and the viral disease in China has had a devastating effect on some fish farms in recent years. To better understand the progression of the viral disease, we combined polymerase chain reaction (PCR) technology and light microscopy with electron microscopy to observe the pathological changes and virus distribution in the gill and head-kidney of diseased fish. Normal crucian carps were infected by injection with tissue filtrate (viral suspension) from naturally infected fish, which caused similar symptoms to those observed in naturally infected fish, and high mortality. The pathogen has the morphological characteristics of a typical herpesvirus (referred to as herpesvirus, CaHV). CaHV can be determined in infected fish tissues, liver, spleen, kidney and head-kidney, using a PCR assay for the major capsid protein (MCP) gene of the known cyprinid herpesvirus. The pathological changes in different tissues, such as the gill and head-kidney, were compared at different times after infection with CaHV. The results showed that CaHV caused varying degrees of pathological change among the various tissues. The pathological changes in the gills and head-kidney increased with time after CaHV infection. There were a large number of virus particles in the head-kidney cells, suggesting that the head-kidney might be the primary target organ for CaHV invasion and replication.