Translational research is progressing toward combined genomic and proteomic analyses of small and precious samples. In our analyses of spinal cord material, we systematically evaluated disruption and extraction techniques to determine an optimum process for the coupled analysis of RNA and protein from a single 5mm segment of tissue. Analyses of these distinct molecular species were performed using micro arrays and high-resolution 2D gels, respectively. Comparison of standard homogenization with automated frozen disruption (AFD) identified negligible differences in the relative abundance of genes (44), with all genes being identified by either process. Analysis on either the Affymetrix or ABI Gene array platforms provided good correlations between the extraction techniques. In contrast, the AFD technique enabled identification of more unique proteins from spinal cord tissue than did standard homogenization. Furthermore, use of an optimized CHAPS/urea extraction provided better protein recovery, as shown by quantitative 2D gel analyses, than did solvent precipitation during TRIzol–based RNA extraction. Thus, AFD of tissue samples followed by protein and RNA isolation from separate aliquots of the frozen powdered sample is the most effective route to ensure full, quantitative analyses of both molecular entities.