Pre-analytical challenges threaten the quality of viral load (VL) testing. This study determined the impact of delayed testing and warmer storage conditions on HIV RNA stability in diagnostic samples. Viral load in samples stored for up to a week reliably differentiated between patients with antiretroviral therapy (ART) suppression and ART failure in the majority of cases. However, this was true when re-centrifugation was done immediately prior to repeat testing in order to avoid contamination of plasma with cellular material, which easily occurs.