Imidazolylpropylguanidines are potent histamine H2 receptor agonists and act as inotropic vasodilators. A large series of 141 derivatives was tested in the isolated guinea pig atrium and submitted to CoMFA. Since all compounds are full compounds are full agonists, pD2 values reflect H2 receptor binding. Hydrophobicity was considered as sigma f of the variable structural moiety, calculated by the Leo-Hansch method. Preliminary Hansch analysis with sigma f, (sigma f)2 and indicator variables showed that pD(2) additively depends on contributions of certain substructures and has a hydrophobic optimum. For CoMFA, all 3D structures were optimized and aligned. Partial Least Squares analysis of pD2 as function of steric and electrostatic field variables and of sigma f and (sigma f)2 led to models with r(2) of 0.78 with and 0.93 without hydrophobicity. Results indicate a parabolic dependence of pD(2) on hydrophobic effects. The 3D distribution of field influences on pD(2) suggests a model (shape and electrostatic potential) of the binding site. The role of branching and different substituent effects of a first and a second ring indicate that adequately branched structures induce a conformational change of the binding site enabling a favourable accommodation of the second ring with various substituents.