Simultaneous quantitation of multiple protein biomarkers within tissue biopsies is a major goal of clinical diagnostics. Although in vitro microarray assays based on fluorescence spectroscopy can probe thousands of potential molecular markers, they discard important anatomical information and introduce numerous artifacts. Multiplexed detection in cells and tissues requires probes with a built-in mechanism for coding a large number of different biomolecules. Extrinsic fluorescent labels yield high detection sensitivity, but spectral overlap due to the relatively broad emission spectra of organic fluorophores and semiconductor quantum dots limits the utility of these technologies in multiplexed in situ applications. We propose a means of molecular profiling directly in tissues with the development of a detection system based on surface enhanced Raman spectroscopy (SERS). At the core of this approach are probes produced by the conjugation of Raman reporter molecules and antibodies to gold nanoparticles, followed by the controlled deposition of silver. The resulting SERS biosensors are biocompatible and highly Raman active. We show that a single excitation light source may be used to obtain spectra from multiple SERS biosensors with prolonged photostability. In addition, the spectra are information-rich with multiple highly resolved peaks. We also demonstrate the ability of the system to identify multiple cancer biomarkers in cultured cells and tissue samples and distinguish normal from cancerous tissues. Finally, we discuss our plans to apply this SERS detection system to the molecular subclassification of clinically heterogeneous but anatomically homogeneous tumors. The combination of highly specific spectra, photostability, and large number of readily available probe components makes this SERS detection system ideal for high-throughput studies of specific biomolecules within tissues. Once optimized, this approach could be applied to the analysis of any disease that reveals itself through molecular perturbations.