Procedures undertaken by NSW Health in the laboratory response to pandemic (H1N1) 2009 influenza were reviewed to assist planning for a future infectious disease emergency. Laboratory plans developed prior to the pandemic sought rapid detection of pandemic virus in the early phases of the pandemic response until demonstration of widespread community transmission, followed then by limited testing when indicated clinically. As planned, the laboratory response was based on the Pandemic Influenza Management System with a web-based outbreak management tool, NetEpi, as the single public health database used for cases and test results. This was found to be effective for tracking specimens and results, and enhanced the public health response. The sustained large volume of community testing during this mild pandemic had an adverse effect on the timely delivery of priority results.