In order to investigate the action point of lignin-carbohydrate complex (Fr4) from Lentinus edodes mycelia extract, DNA microarray analysis was performed, using mouse macrophage-like J774.1 cells. Among seven lignin-carbohydrate complex fractions, Fr4 showed the highest stimulatory activity of tumor necrosis factor production by mouse macrophage-like J774.1 cells, as well as its previously reported anti-HIV activity. Fr4 is composed of lignin precursors such as vanillic acid, syringic acid, p-coumaric acid and ferulic acid, with trace amounts of flavonoids and tannins, and negligible amount of lipopolysaccharides (LPS), confirming the authenticity of Fr4 as a lignin. DNA microarray analysis suggested that Fr4 may affect immune response-related gene expression; however, it may not affect the expression of as many genes as LPS does.