Recent advances in the structural biology of the enzymes involved in fatty acid oxidation have revealed their catalytic mechanisms and modes of substrate binding. Although these enzymes all use coenzyme A (CoA) thioesters as substrates, they share no common polypeptide folding topology or CoA-binding motif. Each family adopts an entirely unique protein fold. Their mode of binding the CoA thioester is similar in that the fatty-acyl moiety is buried inside the protein and the nucleotide portion is mainly exposed to solvent; however, the conformations of the enzyme-bound CoA ligands vary considerably. Furthermore, a comparison of these structures suggests a structural basis for the broad substrate chain length specificity that is a unique feature of these enzymes.