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Abstract: Plant hormone auxin elicits diverse responses in plant growth and development. Accumulated data indicate that the ubiquitin-mediated proteolytic pathway plays a crucial role in transducing auxin signaling. To gain more understanding of the molecular mechanisms underlying auxin action, we performed a comparative transcriptome analysis of auxin responsive genes between Arabidopsis Columbia ecotype and the auxin insensitive mutant eta2 by cDNA-AFLP. Using 256 primer combinations, about 5900 transcript-derived fragments (TDFs) were amplified. Sixty-six differentially expressed TDFs were confirmed by DNA dot blot analysis. Sequence analysis indicated that, a large number of genes involved in transcription regulation or RNA metabolism were identified as auxin-regulated genes. Northern blot analyses confirmed transcription levels of 16 auxin-regulated genes. These genes include various forms of transcription regulators, defense related, RING-type ubiquitin ligases, and glycosyl hydrolase. This study demonstrates that auxin exerts its effect in complex transcriptional networks. [Copyright &y& Elsevier]