The Ontario Public Health Laboratories system (OPHL) is in the midst of a six-year plan to implement molecular tools for pandemic influenza diagnostics in one central and three regional public health laboratories. This plan has been formulated as a consequence of: 1) experiences gained through severe acute respiratory syndrome (SARS), and comments of the members of the Expert Panel on SARS and Infectious Disease Control (i.e., the Walker report); 2) a review of pandemic preparedness literature; 3) historical and epidemiologic discussions about previous pandemics; and 4) suggestions made by various pandemic working committees. The OPHL plan includes: 1) an aggressive restructuring of the overall molecular microbiology testing capacity of the OPHL; 2) the ability to shift influenza testing of samples between designated OPHL laboratories; and 3) the development of screening tools for pandemic influenza diagnostic tests. The authors believe that investing in increased molecular testing capacity for regional laboratories outside the greater Toronto area will be beneficial to the OPHL system whether or not an influenza pandemic occurs. Well-trained technologists and microbiologists, and the introduction of new technologies, will facilitate the development of a wide variety of molecular tests for other infectious diseases at public health laboratories geographically distant from Toronto, thus enhancing overall laboratory testing capacity in the province of Ontario.