The water extract of Scutellariae baicalensis Georgi (S. baicalensis) has potential anti-tumor and anti-inflammatory activities. A major flavonoid isolated from S. baicalensis, baicalein, was also found to have anti-tumor and anti-inflammatory activities. These biological activities could be due to their antioxidant action and/or effect on different signal transduction pathways. We investigated the effects of several baicalein analogs with a substitution of hydrogen of the hydroxyl group at the 6th position of A ring on three signal pathway mediated transcription (NF-kappaB, AP-1, and CREB) associated with inflammation and cancer growth. We found that the analogs with O-alkyl group of the different carbon chain length or O-benzyl activated NF-kappaB transcription without TNFalpha stimulation. Some of the analogs increased TNFalpha stimulated NF-kappaB transcription by two- to threefold. None of the analogs studied has major effect on AP-1 signal transduction with or without TPA stimulation. All of the analogs increased CREB transcription with forskolin stimulation up to twofold. However, they did not have a potent effect (less or about twofold activation) on intrinsic CREB signal transduction. The modification of baicalein at the 6th position of A ring was not correlated with change in these signal transduction pathways and cytotoxicity. Though, they are structural analogs, they are not functional analogs. Modification of baicalein at the 6th position could alter the specificity of action toward different cellular targets. Flavonoids could be chemophores in the development of drugs targeted at different signal transcriptional pathway.