Kuchijirosho is a lethal infectious disease of fugu Takifugu rubripes, and the causative pathogen has been predicted to be an RNA virus. Although the homogenate of kuchijirosho-affected brain is pathogenic to fugu, the suspected viral particles have not been found in the brain and the viral genome has not been isolated. We attempted to clone the cDNA of the kuchijirosho virus genome using the Rapid Determination System for Viral RNA Sequence method. Three cDNA segments of ca. 1,000 nt each, which could be parts of the viral genome, were obtained from total RNA extracted from the brains of fugu artificially infected with kuchijirosho. According to RT-qPCR, the brain had more of these three kuchijirosho-associated RNAs (KARs) than any other tissues. KARs in the brain were detected 1-2 days after injecting the homogenate of kuchijirosho-affected brain and KARs expression levels were increased rapidly until death. These results show that the detection of KARs can be sufficiently effective for the molecular diagnosis of kuchijirosho. Even if KARs are parts of the viral genome, it is unclear to which taxonomic family the kuchijirosho virus belongs, because the nucleotide sequences of KARs did not correspond to those of any other organisms including viruses.