The natural antisense transcripts (NATs) may cause RNA masking, RNA editing, RNA interference, alternative splicing and translational regulation amongst other effects. Over 2500 mammalian NATs are have been found recently. In recent investigations indicate that there is a relationship between sense-antisense RNA expression and tissue-specific RNA expression. We also identified cis-NATs in mouse, rat, fruit fly, nematode and arabidopsis genomes by the same methodology. We identified cis-NATs in 6 organisms, and found 15253, 2572, 1159, 239, 391 and 272 NAT clusters in human, mouse, rat, fruit fly, nematode and arabidopsis genomes respectively. In tissue-specific human natural antisense transcripts, there are 3,394 NATs (LOD>2). Tissue-specific NATs in the mouse genome were also found. In this article, we present our tissue-specific natural antisense transcripts database (ATTdb) and provide a user-friendly interface for visualization. ATTdb enables detailed and visual information of NATs in six organisms. Tissue-specific NATs are also available in ATTdb.