Herpes zoster (HZ) is a neurocutaneous disease caused by Varicella-zoster virus (VZV) as a consequence of declined cell-mediated immunity, immune suppression and immunodeficiency. As reactivation of JC polyomavirus (JCPyV) might be linked with immunodeficiency or immunosuppressive therapy, the relationship between HZ and JCPyV reactivation was investigated. The incidence of JCPyV in urine samples from 102 patients with HZ and 100 healthy individuals from South Korea was determined by PCR. The incidence values for HZ patients and control individuals did not differ significantly (24.5% vs. 20.0%, respectively, P = 0.5391). When different age groups were monitored, the positivity values of 21.1%, 20.0%, and 30% were found for 20-39, 40-59 and over 60 year-old patients, respectively. In order to determine the genotype of JCPyV isolates, their VP1-large T antigen (VT)-intergenic region was PCR amplified, sequenced and analyzed. Three distinct types, namely 1, 2A and 7B were found in 8%, 24%, and 68% of were found among 25 isolates from HZ patients. Using phylogenetic analysis, the type 1 isolates were assigned to the 1C subtype. These results indicate that HZ does not play an important role in JCPyV reactivation and is not associated with JCPyV.