Development of diagnostic methods for rapid and sensitive identification of viruses is essential for the advancement of therapeutic and preventive intervention strategies. Current diagnostic methods, e.g. virus isolation, PCR, antigen detection and serology, are time-consuming, cumbersome, or lack the required sensitivity. We have investigated the use of aligned Ag nanorod arrays, prepared by oblique angle deposition (OAD), as surface-enhanced Raman scattering (SERS) substrates for the identification and quantitation of viral pathogens. The OAD method of substrate preparation facilitates the selection of nanorod size, shape, density, alignment, orientation, and composition. The current chapter () will address the fundamental nanostructural design of metallic nanorod arrays and their influence on SERS enhancement, as well as the development of a spectroscopic biosensor assay for virus detection based on these unique nanostructured SERS probes. We will also present results of multivariate statistical analysis on the SERS spectra of different viral strains that indicate its feasibility to differentiate and classify viruses based on their intrinsic SERS spectra. © 2009 American Chemical Society.