To establish a rapid high-throughput evaluation system for the enhanced plant growth-inhibitory activity caused by modifications of <i>cis</i>-cinnamic acid's (<i>cis</i>-CA's) chemical structure, a DNA microarray assay was used to analyze the changes in early gene responses of <i>Arabidopsis thaliana</i> seedlings. After a 6-hr exposure to (<i>Z</i>)-3-(3-iodophenyl)acrylic acid, we observed an upregulation in three classes of early auxin-responsive genes, which was similar to the transcriptional response to indole-3-acetic acid (IAA), together with an upregulation of the genes related to environmental stress and toxin detoxification responses. Gene responses to 2-(3,4-dihydronaphthalen-1-yl)acetic acid were similar to those to IAA. In contrast, fewer genes were upregulated in response to its double-bond isomer, (<i>Z</i>)-2-[3,4-dihydronaphthalen-1(2<i>H</i>)-ylidene]acetic acid, than to <i>cis</i>-CA. DNA microarray data suggest that the structurally different <i>cis</i>-CA analogues trigger diverse gene responses.