Taxus sp. cell culture for the production of the anti-cancer agent paclitaxel was used as a model system to investigate the effects of aggregate size on secondary metabolite accumulation. We developed a method to separate and subsequently screen different aggregate size fractions for paclitaxel and related taxanes using high performance liquid chromatography (HPLC). Aggregation dynamics in the culture system were phenomenologically described using a mathematical simulation correlated with experimental data. We used electrical zone sensing in conjunction with image analysis to collect aggregate size distribution data, and tracked the evolution of this distribution over the batch culture period. The model was formulated in a population balance equation framework, which could be directly compared to the distribution data collected. The comparison of the data and the model was used as meaningful criteria to evaluate the basic assumptions regarding aggregation phenomena that were used in structuring our model. This enhanced understanding of culture behavior can eventually be used as a tool to guide culture conditions to increase product accumulation.