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Progressive multifocal leukoencephalopathy (PML) is the well\u2010known disease caused by the virus. It has also been associated with nephropathy and tumorogensis. At present, based on <jats:italic>vp1<\/jats:italic> capsid gene 7 genotypes have been detected. Genetic variations of JC virus in different geographical areas and the presence of different subtypes is a useful tool for reconstructing of the genetic information of JC virus and understanding of its evolution. The aim of this study was to investigate different genotypes of the JC virus in the urine of 100 kidney transplant recipients, 43 rheumatoid arthritis patients, and 100 healthy individuals as control group in Isfahan. DNA was extracted by phenol\u2010chloroform method and subjected to a nested PCR using specific primer for <jats:italic>vp1<\/jats:italic> capsid gene designed by Oligo 7 software. Fisher's exact test was used for statistical analyses. Using MEGA 6 software the sequences were aligned using Clustal W tool and phylogenetic trees were constructed by neighbor joining method. Thirty\u2010one positive samples were sequenced. Genotypes 1, 3, and 4 of the virus were detected for the first time in Iran. For the first time genotype 3 was reported as the dominant genotype in Iran. For the first time in the world, genotype 4 was detected in rheumatoid arthritis patients. <jats:bold><jats:italic>J. Med. 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