HNF4α is an orphan member of the nuclear receptor family with prominent functions in liver, gut, kidney and pancreatic β cells. We have solved the x-ray crystal structure of the HNF4α ligand binding domain, which adopts a canonical fold. Two conformational states are present within each homodimer: an open form with α helix 12 (α12) extended and collinear with α10 and a closed form with α12 folded against the body of the domain. Although the protein was crystallized without added ligands, the ligand binding pockets of both closed and open forms contain fatty acids. The carboxylic acid headgroup of the fatty acid ion pairs with the guanidinium group of Arg 226 at one end of the ligand binding pocket, while the aliphatic chain fills a long, narrow channel that is lined with hydrophobic residues. These findings suggest that fatty acids are endogenous ligands for HNF4α and establish a framework for understanding how HNF4α activity is enhanced by ligand binding and diminished by MODY1 mutations.