The crystal structure of the food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b] pyridine (PhIP) has been determined by single-crystal X-ray crystallography. Crystals grown by evaporation of an aqueous solution form in the monoclinic space group P2(1)/n with two molecules of PhIP per asymmetric unit, along with six water molecules. The phenyl groups of these two PhIP molecules have torsion angles of different magnitude with respect to the plane of the imidazopyridine moiety. To maintain centrosymmetry, the crystal also contains an oppositely torsioned symmetry equivalent of each. The amino groups of both PhIP molecules take part in an extensive hydrogen bond network with the water of crystallization, forming long channels through the crystals parallel to the crystallographic b axis. The diffraction results are compared to theoretical calculations of the optimized geometry for a single PhIP molecule in vacuo as well as with water hydrogen-bonded to the exocyclic amine. In general, the agreement between the X-ray crystal structure of PhIP and its theory-derived counterpart in vacuo is within the combined experimental-theoretical uncertainty. The C-N bond to the exocyclic amine and the neighboring C=N imidazole bond are exceptions. This is attributed to the combined neglect of the crystal environment, waters of hydration, and the lack of coplanarity between the imidazole ring and the amine group in the calculations. To address the effect of waters of hydration, additional calculations were performed to optimize the geometry of a PhIP molecule with two water molecules hydrogen-bonded to the exocyclic amine. The resulting C-N exocyclic amine and C=N imidazole bond lengths were closer to those obtained by X-ray diffraction. The accord between theory and experiment demonstrates the utility of applying theory to (1) accurately predict structures of PhIP metabolites and intermediates that are too labile for study by conventional structural techniques such as X-ray crystallography and (2) assist in studying the mechanisms by which PhIP and its metabolites interact with proteins and DNA.