Many people suffer from allergies, such as asthma, pollinosis and atopic dermatitis, as well as inflammatory diseases. To elucidate the anti-allergic and anti-inflammatory effects of food components, we developed a DNA microarray carrying genes related to immunity, inflammation and housekeeping. Results of gene expression analysis using the DNA microarray showed good reproducibility and correlated well with those of quantitative RT-PCR analysis. DNA microarray analysis showed that the butanol soluble fraction of bitter gourd placenta extract suppressed bacterial lipopolysaccharide (LPS)-induced inflammatory gene expression in mouse macrophage-like cells (RAW264.7). DNA microarray analysis demonstrated that the flavonoid fisetin suppressed the activated T cell membrane induction of gene expression in HMC-1 human mast cells. Thus, we demonstrated the anti-inflammatory effect of bitter gourd and anti-allergic effect of fisetin using DNA microarray analysis. Furthermore, DNA microarray analysis detected gene expression associated with skin irritation using a reconstructed human epidermal model.