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A fast, accurate method of assigning partial atomic charges is described. The method is based upon the concept of electronegativity equalization and is parametrized to fit electrostatic potentials obtained from ab initio quantum calculations. A novel algorithm for identifying alternate resonance forms is used to ensure that chemically equivalent atoms are assigned equal charges. The resulting charges are independent of conformation, yield good agreement with ab initio electrostatic potentials, and are similar to standard force field charges for common biochemical components. The method is broadly parametrized and generates charges for a drug-like compound in about 0.45 s on a 2.26 GHz Pentium 4 PC. It should thus be useful in a range of applications, such as molecular design and QSAR. The resonance algorithm is expected to have additional applications, such as in atom-typing and detection of molecular symmetry.