Viral load testing for hepatitis C virus (HCV) RNA has become a key parameter in the diagnosis of infection and treatment monitoring. This study evaluated the performance characteristics of the MultiCode-RTx HCV assay (MultiCode; EraGen Biosciences, Inc., Madison, WI), a real-time PCR test targeting the 3′ untranslated region (UTR) of the HCV genome, compared to the TaqMan HCV load ASR assay (TaqMan; Roche Diagnostics, Indianapolis, IN) that targets the 5′ UTR. For plasma specimens, the MultiCode assay had a limit of detection of 2.3 log10 IU/ml and a linear range of at least 6.7 log10 IU/ml. Comparison of plasma viral loads obtained by the MultiCode and TaqMan tests showed that they were in very close agreement (mean difference, −0.1 log10 IU/ml). No genotype bias was observed for genotypes 1, 2, and 3. When the MultiCode assay was evaluated with the MagNA Pure and easyMAG extraction methods, the viral loads for the easyMAG extraction were consistently higher for all specimens tested (mean difference, 0.45 log10 IU/ml). Aside from the limit of detection, the performance characteristics of the MultiCode assay were similar to the TaqMan assay for the clinical application of HCV load testing.