To investigate the comprehensive effects of polyunsaturated fatty acids (PUFA) on gene expression, we analyzed changes of mRNA expression in PUFA-treated HepG2 cells using a DNA micro array. We incubated HepG2 cells for 24 h with or without 0.25 mM oleic acid (OA), arachidonic acid (AA), eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA), and then compared the expression profiles of thousands of genes using a GeneChip. PUFA influenced the expression of various genes related to cell proliferation, growth and adhesion, as well as for many transcription factors including sterol regulatory element binding proteins (SREBP). Treatments with AA, EPA, and DHA repressed the expression of genes related to cholesterol and lipid metabolism. Moreover, data from gene chip analysis proved that PUPA reduced the expression ofprostasin, which is a serine protease. By measuring the mRNA levels of SREBPs, mevalonate pyrophosphatase and prostasin using quantitative RT-PCR, we confirmed the effect of PUFA revealed by gene chip analysis. These data might provide useful clues with which to explore novel functions of PUPA.