A standardized, combined flavonoid extracts of Scutellaria baicalensis and Acacia catechu, UP446, demonstrates favorable anti-inflammatory properties. In this study, DNA microarray, quantitative polymerase chain reaction (QPCR), and enzyme-linked immunosorbent assay (ELISA) were used to study the effect of UP446 on the lipopolysaccharide (LPS)-induced pro-inflammatory gene regulation of both animal and human immortalized cell lines and also primary human cells. One consistent result from microarray was that the gene expression levels stimulated or suppressed by LPS were returned to normal levels by the UP446 co-treatment. This normalization effect from UP446 was also shown for pro-inflammatory genes cyclooxygenase (COX)-2, tissue necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6 using QPCR, and TNF-α using ELISA. The controlling transcriptional factor of these genes, NFκB, was also down-regulated by UP446 in the LPS-induced cell models. Microarray analysis for numerous genes, including cytokines, chemokines, receptors, transcriptional factors, caspase, growth factors, and phosphatases, suggests not only a genomic anti-inflammatory activity for UP446 but also signaling pathways of cell proliferation, cell death, and lipid metabolism demonstrated on different types of cells.