The effect of fatty acyl CoA and fatty acid on the solution structure and dynamics of two intestinal enterocyte fatty acid binding proteins, intestinal (I-FABP) and liver (L-FABP), was examined by time-resolved fluorescence of FABP aromatic amino acid residues. I-FABP Trp displayed two rotational correlation times, 6.6 and 0.4 ns. reflecting motion of the protein as a whole and segmental mobility of Trp. Neither oleoyl CoA, oleic acid, nor CoASH altered overall I-FABP rotational correlation time. However, oleic acid and CoASH increased I-FABP Trp segmental mobility, while oleoyl CoA and CoASH decreased I-FABP Trp limiting anisotropy (order). The angle of I-FABP Trp "wobbling in a cone" was increased by ligands in the order oleoyl CoA > CoASH > oleic acid. L-FABP Trp segmental mobility. L-FABP overall rotational motion, in contrast to that of I-FABP, was significantly increased by ligands in the order oleoyl CoA > oleic acid > CoASH. cis-Parinaric acid and cis-parinaroyl CoA bound to L-FABP also reflected overall L-FABP motion but yielded longer rotational correlation times, 8.2 and 10.7 ns, than the respective apo-FABPs. Such effects were not observed with I-FABP. Finally, both cis-parinaric acid and cis-parinaroyl CoA were much less ordered in the I-FABP ligand binding site than with L-FABP. These observations suggest that the rotational dynamics of L-FABP and its conformation are more sensitive to ligands than I-FABP. Further, ligands such as fatty acids, fatty acyl CoAs, and/or CoASH differentially modulate the I-FABP and L-FABP dynamics, and the ligand binding sites of these proteins differ in their ability to order the ligands.