Given the new diagnostic need following the pandemic caused by the A(H1N1)v virus, we evaluated the performance characteristics of Xpert® Flu assay (Cepheid). The overall sensitivity and specificity were 65.6% and 92.8%, respectively. Sensitivity and specificity for A(H1N1)v virus were 85.7% and 94.9%, respectively, and therefore the Xpert® Flu assay is suitable for a rapid diagnosis in critically ill patients where diagnosis is crucial for clinical management and for an appropriate public health response.