Transient expression systems are intensively used to study the transactivation potential of transcription factors and to confirm target promoters. Here we present a novel system based on the high-efficiency transformation of cultured Arabidopsis thaliana cells by agrobacteria. To demonstrate the potential of this system, we compared it with a commonly used protoplast transfection assay, and studied the regulation of phenylpropanoid biosynthetic pathway genes by various transcription factors. Both systems led to comparable results on the regulation of the promoters tested. However, the agrobacterium-mediated co-transformation assay needs significantly less time, requires only mixing of cultured plant cells with agrobacteria, is less labour-intensive and allows handling of multiple assays in parallel, making it suitable for medium- to high-throughput analyses. In addition, the binary vectors used are the same for both cell-based assays and stable plant transformations.