Methodology of building up and validation of models for carcinogenic potentials of drugs by means of the CORAL software is described. The QSAR analysis by the CORAL software includes three phases: (i) definition of preferable parameters for the optimization procedure that gives maximal correlation coefficient between endpoint and an optimal descriptor that is calculated with so-called correlation weights of various molecular features; (ii) detection of molecular features with stable positive correlation weights or vice versa stable negative correlation weights (molecular features which are characterized by solely positive or solely negative correlation weights obtained for several starts of the Monte Carlo optimization are a basis for mechanistic interpretations of the model); and (iii) building up the model that is satisfactory from point of view of reliable probabilistic criteria and OECD principles. The methodology is demonstrated for the case of carcinogenicity of a large set (n = 1464) of organic compounds which are potential or actual pharmaceutical agents.