We study Taxus suspension cultures for production of the anti-cancer agent paclitaxel (Taxol™). At the molecular level, we have examined mRNA expression to clarify genetic regulation of the paclitaxel secondary metabolic pathway in both whole cultures and isolated cell sub-populations, and have developed transformation methods to study and manipulate pathway genes. At the population level, we have developed methods to isolate individual particles (e.g., cells, protoplasts, nuclei) from Taxus suspension cultures and using flow cytometry have identified specialized cell sub-populations with characteristic growth and paclitaxel production patterns. At the culture process level, we have identified cell aggregation as a key property affecting system behavior, and have established methods to both experimentally characterize and mathematically describe aggregation and its influence on culture performance. An integrated approach that optimizes at all functional scales is necessary to establish superior plant cell culture processes for production and supply of important bioactive secondary metabolites.