We compared two novel Qiagen QS-RGQ viral load assays with the established Abbott RealTime assays on a highly diversified panel of 121 human immunodeficiency virus (HIV) and 107 hepatitis C virus (HCV) specimens. The quantifications correlated well for all HIV and HCV types, but Qiagen yielded higher HCV concentrations than Abbott, predominantly in genotypes 4 and 5.