To better understand the regulatory networks that control plant gene expression, tools are needed to systematically analyze and visualize promoter regulatory sequences in Arabidopsis thaliana. We have developed the Athena database, which contains 30,067 predicted Arabidopsis promoter sequences and consensus sequences for 105 previously characterized transcription factor (TF) binding sites. Athena provides four novel tools to facilitate the analysis of promoter sequences: a promoter visualization tool to enable the rapid inspection of key regulatory sequences in multiple promoters, a TF binding site enrichment tool to identify statistically over-represented TF sites occurring in a user-selected subset of promoters, a data-mining tool to rapidly select promoter sequences containing the specified combination of TF binding sites, and a tool to display the distribution of TF binding site positions in a selected set of promoter sequences.