Background: Hepatitis C virus (HCV) infection is one the major health concern among the infected transplant patients. Considering several complications of the disease in them, pre and post-transplantation studies should be performed for monitoring of the infection, as well as, developing new treatment protocols. Objectives: The current study was conducted to determine the Hepatitis C Virus RNA level among seropositive liver and kidney transplant recipients in Namazi Hospital; the main transplantation center in southern Iran. Materials and Methods: RNAs were extracted from 105 serum samples of seropositive liver and kidney transplant recipients and analyzed by Real-time PCR assay using a set of primers. Results: HCV RNA was detected in a total of 46/105 (43.8%) recipients' serum samples [39/46 (84.8%) males and 7/46 (15.2%) females]. Moreover, 8/46 (17.4%) and 38/46 (82.6%) were kidney and liver recipients, respectively. The copy number of HCV RNA, measured by the Real-time PCR assay, ranged from 5 × 102 to 3.14 × 109 copies/mL; Median 2.37 × 105 copies/mL and 1.7 × 103 to 9.44 × 104 copies/mL; Median 2.89 × 104 copies/ mL in liver and renal transplant patients, respectively. The comparison of viral load between liver pre transplant recipients group and post transplant counterpart indicated that the copy number of HCV RNA was significantly higher in the post transplant recipients (P = 0.033). The prevalence of the viral nucleic acid was significantly higher in males than in females (P = 0.026). Similarly, with regards to the age groups, the prevalence of HCV RNA was significantly higher in age group ≥ 45 years than age group < 45 years (P = 0.028). Conclusions: Considering the results, it can be concluded that HCV RNA detection is strongly suggested in transplant patients group to determine the prevalence of the disease and their responses to antiviral therapy and diagnosis of drug resistance. In addition, continuous and regular surveillance of HCV RNA level in such patients is highly recommended in order to better manage the complications of graft loss and reduce the mortality rate. Further studies are needed to find new therapeutic methods to lower the incidence of infection of new healthy allograft tissues in HCV RNA positive recipients.