Procalcitonin (PCT) has been reported to differentiate between bacterial and viral causes of respiratory tract infections. We aimed to assess its ability to discriminate between viral and bacterial infection during the H1N1 pandemic of 2009. The design of this study was a retrospective single centre case series review. Subjects were 17 adult patients admitted to the intensive care unit with suspected or confirmed isolated H1N1 influenza infection, from whom a PCT level was assessed within 24 hours of admission. All patients were admitted during the H1N1 pandemic in Queensland from 6 July 2009 to 2 August 2009. The relationship between PCT levels and H1N1 status was measured by a Wilcoxon rank sum test. Patients were proven to have isolated H1N1 infection as judged by Polymerase Chain Reaction, with no bacterial super-infection. Of this number, 37% had a PCT <1 microg/l, and 63% of patients had an indeterminate PCT between 1 and 10 microg/l. The demographics of all 17 patients were mean age 48.2 years (SD 13.6 years); 59% female; mean Acute Physiological and Chronic Health Evaluation II score 20.3 (SD 5.8); mean intensive care unit 477.5 hours (SD 330.0 hours); 82% of cases required mechanical ventilation; 24% of cases required extracorporeal membrane oxygenation and 94% of cases were alive at intensive care unit discharge. PCT was neither sensitive nor specific in determining isolated H1N1 infection in this series of patients. The use of PCT to assist in isolation triage of patients suspected of infection with H1N1 influenza in the intensive care unit should be made with caution. A larger study may be required.