The natural hosts regarding Orthohantaviruses are rodents, soricomorphs and bats, and it is well known they may cause serious or even fatal diseases among humans worldwide. The virus is persistent among animals and it is shed via urine, saliva and feces, throughout the entirety of their lives. We aim to identify the effectiveness regarding hantavirus detection from rodent tissue samples and urine originating from naturally infected rodents. Initially, animals were trapped at five distinct locations throughout the Transdanubian region in Hungary. Lung, liver, kidney and urine samples were obtained from 163 perished animals. All organs and urine were tested using nested reverse transcriptase-polymerase chain reaction (nRT-PCR). Furthermore, sera were examined for IgG antibodies against DOBV and PUUV viruses by Western Blot assay. IgG antibodies against hantaviruses and/or nucleic acid were detected in 25 (15.3%) cases. Among Apodemus, Myodes, and Microtus rodent species, DOBV, PUUV, TULV were all clearly identified. The virus nucleic acid was detected most effectively from the kidney (100%), while only 55% of screened lung tissues were positive. Interestingly, only 3 out of 20 rodent urine samples were positive regarding nRT-PCR. Moreover, five rodents were seropositive without detectable virus nucleic acid from any of the tested organs.