Objective: To evaluate the sensitivity and specificity of influenza virus detection by two commercial reverse transcriptase PCR methods compared with a reference real-time PCR. Methods: 122 clinical specimens were tested on Xpert® Flu and RealStar® Influenza Screen & Type. A reference real-time RT-PCR, at a specialist laboratory was chosen as the gold standard for comparison. Results: RealStar® Influenza Screen & Type had higher sensitivity for influenza A and influenza B respectively (92.3% and 88.2%) when compared to Xpert® Flu (78.8% and 76.5%). Both tests had excellent specificity. Conclusions: The simplicity and speed of the Xpert® Flu system could allow it to be used in the near-patient setting; however in circumstances where excluding a diagnosis of influenza may be critical, negative specimens may need to be repeated using a more sensitive assay.