A new class of nonlithographically prepared surface enhanced Raman spectroscopy (SERS) substrates based on metalized, nanostructured poly(p-xylylene) films has been developed and optimized for surface plasmon response with a view to applications of SERS detection of microbial pathogens, specifically, bacteria and viruses. The main emphasis has been on achieving high spot to spot, sample to sample reproducibility of the SERS signals while maintaining useful enhancement factors. The use of these surfaces, metalized with either Ag or Au, provides a noninvasive and nondestructive method for spectral fingerprint analyses of both bacteria and viruses. Examples are given for the detection of bacteria (E. coli and B. cereus) and viruses (respiratory syncytial virus and Coxsackievirus). Our method is able to distinguish Gram positive from Gram negative bacterial strains as well as enveloped and nonenveloped viruses. The results demonstrate the development of a new class of SERS substrates which can provide rapid, selective identification of infectious agents without amplification of cultures.