The recovery efficiency of naked poliovirus-RNA in water using virus concentration methods was determined to evaluate the possibility of detecting naked viral genomes. Two conventional virus concentration methods (1MDS-method and HA-method) and two methods developed by our research group (Mg-method and Al-method) were applied to recovery tests of poliovirus-RNA from four kinds of water sample, in parallel with recovery tests of poliovirus-virions. Mean recovery yields of poliovirus-RNA by the Mg-method were 5.7, 12, 3.4, and 17% for MilliQ water, tap water, secondary-treated sewage, and seawater, respectively. Meanwhile, mean recovery yields of poliovirus-virions by the Mg-method were 6.6-14.7 times higher than those of the RNA. Using the Al-method, poliovirus-RNA in MilliQ water and tap water was recovered at a higher recovery yield as compared to the Mg-method (69% from MilliQ water and 26% from tap water on average) in addition to the virions. The 1MDS-method and the HA-method did not provide as high recovery yields of the virions as the Mg-method. From these results, the Mg-method was judged most appropriate for selective detection of virions instead of naked viral genomes in water among the four methods tested.