It is vital that auditing tools used by researchers and managers yield valid assessments and meaningful comparisons irrespective of the organisational setting. The Quick Scan Audit Methodology (QSAM) offers such a systematic approach by utilising multiple data collection methods and a codified value stream uncertainty measure to assess supply chain performance. Although previously only employed within the private sector, this article explores the use of QSAM to benchmark the pharmaceutical value streams in eight Australasian public sector hospitals, which are best characterised as having multi-layered and complex subsystems. Transferability of the QSAM methodology to public healthcare supply chains is critiqued and needed modifications are described. The audits also reveal that high levels of system uncertainty are negatively impacting the provision of critically important healthcare supplies.