Novel methods for predicting logP, pK(a), and logD values have been developed using data sets (592 molecules for logP and 1029 for pK(a)) containing a wide range of molecular structures. An equation with three molecular properties (polarizability and partial atomic charges on nitrogen and oxygen) correlates highly with logP (r2 = 0.89). The pK(a)s are estimated for both acids and bases using a novel tree structured fingerprint describing the ionizing centers. The new models have been compared with existing models and also experimental measurements on test sets of common organic compounds and pharmaceutical molecules.