Butyrates effects on the immune system are mediated through the inhibition of class I histone deacetylases and activation of its G-protein coupled receptor targets: Hydroxycarboxylic acid receptor 2| (GPR109A), FFAR2 (GPR43), and FFAR3 (GPR41). Among the short-chain fatty acids, butyrate is the most potent promoter of intestinal regulatory T cells in vitro' and the only one among the group that is an  ligand. It has been shown to be a critical mediator of the colonic inflammatory response. It possesses both preventive and therapeutic potential to counteract inflammation-mediated ulcerative colitis and colorectal cancer.
Butyrate has established antimicrobial properties in humans that are mediated through the antimicrobial peptide LL-37, which it induces via HDAC inhibition on histone H3. In vitro, butyrate increases gene expression of FOXP3 (the transcription regulator for ) and promotes colonic regulatory T cells (Tregs) through the inhibition of class I histone deacetylases; through these actions, it increases the expression of interleukin 10, an anti-inflammatory cytokine. Butyrate also suppresses colonic inflammation by inhibiting the IFN-γ–STAT1 signaling pathways, which is mediated partially through histone deacetylase inhibition. While transient IFN-γ signaling is generally associated with normal host immune response, chronic IFN-γ signaling is often associated with chronic inflammation. It has been shown that butyrate inhibits activity of HDAC1 that is bound to the Fas gene promoter in T cells, resulting in hyperacetylation of the Fas promoter and up-regulation of Fas receptor on the T-cell surface.
Similar to other  agonists studied, butyrate also produces marked anti-inflammatory effects in a variety of tissues, including the brain, gastrointestinal tract, skin, and vascular tissue. Butyrate binding at FFAR3 induces neuropeptide Y release and promotes the functional homeostasis of colonic mucosa and the enteric immune system.