In this evaluation we compare an existing in-house HSV and VZV assay (Roche MagNAPure LC/LightCycler 1.0) with the AusDiagnostics Herpes assay (Roche MagNAPure 96/High-Plex 384-well Analyser) for detection of HSV/VZV in clinical samples. The AusDiagnostics Herpes Assay (AusDx) demonstrated a significant increase in sensitivity (> 2 log10) compared to the in-house reference method with a five-fold decrease in sample input volume (0.2 mL compared to 1.0 mL). To determine the utility of each method to detect experimental mixed HSV infections, controls containing HSV-1 and HSV-2 were titrated against one another at various concentrations in a chequerboard experiment. The AusDx assay was able to detect both high and low concentrations of HSV-1 and HSV-2 (and vice-versa) for all controls tested. The reference method was unable to detect low concentrations of one target when the other target was high. Fifty clinical samples were tested in a blinded prospective manner. AusDx assay demonstrated 100% sensitivity and specificity with the reference method. Assessment of assay reproducibility (extraction and PCR) was performed using the quantitative result output from replicates of an extraction control and a DNA control containing known concentrations of HSV-1, HSV-2 and VZV. The AusDx assay demonstrated good assay reproducibility across all targets. The AusDx assay was also assessed for well-to-well contamination by alternating VZV high-positive controls with negative controls. Well-to-well contamination was not observed. The AusDx assay has a sample adequacy control (human house-keeping gene) and internal control (artificial DNA) to determine sample quality and inhibition. Inhibition was not observed in the patient samples tested, however a varying degrees of sample quality were noted. Total consumable costs (extraction and PCR) of the in-house assay were also comparable with the AusDx assay. The AusDx assay has added advantages such as less hands-on time (20min compared to 45min), automated set-up, sample adequacy control, and additional targets (Enterovirus, Adenovirus group B, C, E and Cytomegalovirus). Overall the AusDx out-performed the reference method.