Influenza is a constant concern in public health, from the yearly task of selecting vaccine strains to the emerging threat of a pandemic strain. Our lab is developing a suite of diagnostic microarrays to aid global strain surveillance efforts. The first generation FluChip demonstrated the ability to rapidly type and subtype commonly circulating human viruses, as well as the potentially pandemic H5N1 avian viruses. Results were obtained in 9 hours, while traditional subtyping methods require several days, minimum. The second generation of chips currently being evaluated in our lab builds on the success of the original FluChip while expanding the scope of inquiry beyond subtyping. The time needed to subtype influenza can be cut to 7 hours by considering a single, non-antigenic internal gene that appears to co-evolve with the external genes. Efforts are underway to provide a complete characterization of influenza B viruses, including the ability to distinguish between the two major lineages currently circulating. A proof of concept chip to detect single base mutations that confer resistance to antiviral compounds has been developed. Detection of polygenic traits such as pathogenicity and host range are also being explored. Results from this second generation of FluChips will be presented and the potential contributions of inexpensive low-density microarrays to strain surveillance will be discussed.