Genome-scale approaches like DNA microarrays have made enormous contributions in basic research fields like cancer biology; yet there are few published examples of their applications to industrial bioprocess characterization. To an extent, this can be attributed to the absence of significant genomic resources for industrially relevant cell types and the consequent paucity of meaningful gene/protein annotations. In this presentation, we use the example of a Baby Hamster Kidney (BHK) cell based process to demonstrate that, despite such limitations, one can extract useful process information from genome-scale technologies. We show that cross-species hybridization of BHK samples on Chinese Hamster Ovary (CHO) DNA microarrays is a practical and feasible approach for bioprocess characterization. The resulting data can be used to fingerprint bioreactor cultures to demonstrate process equivalence or lack thereof. Such technologies have the potential to substantially increase the size of the “physiological state vector” from a handful of physical process parameters that traditionally define a bioprocess.