The Golgi complex is the central organelle in the secretory membrane trafficking and its organization strongly depends upon the flow of coming and leaving material. The principles of cargo transfer to, through, and away from the Golgi complex were investigated in numerous studies. However, the knowledge of how the Golgi complex responses to changes in diverse trafficking events (e.g., ER exit block) on a molecular level is far from being complete. In order to identify regulatory molecules playing a role in the dynamic organization of the Golgi complex, we established a fluorescent microscopy-based quantitative assay to measure rates of the Golgi redistribution and assembly after addition and washout of BFA, respectively. At first, we tested our system under the condition of over-expression of GFP-tagged proteins. We measured their influence upon BFA-induced effects in a format, suitable for large-scale studies in living cell, namely cell arrays. The approach can be applied for large-scale RNA interference studies as well as for chemical screening.