A method is described for the prediction of the retention index (I) from chemical structure, using the number of atoms in the molecule (Z), the I increment for atom addition (A) and the group retention factors (GRFs) of the functional groups and substituents. This method can predict the retention indexes of a wide range of compounds, such as acids, alcohols, amines, acid esters, aldehydes, ketones, ethers, aromatic hydrocarbons, alicyclics, heterocyclics, etc. on polar as well as non-polar columns to within 3% error. Accurate A and GRF values are essential to the prediction. These values can be obtained from homologous series, but a system of arbitrarily assigned A value and adjusted GRFs are also used. The GRFs of the substituents and functional groups depend on the polarity and polarizability of the analyte and the stationary phase and also on the molecular connectivity of the atoms, namely, primary, secondary and tertiary carbon atoms or hydrogen atoms, to which these groups are attached. Highly polar and polarizable groups can alter the A value. When the functionality of a group is masked by substitution, the analyte molecule will tend to behave chromatographically like hydrocarbons. The difficulty in predicting the I values of compounds of multi-functionality by the rule of additivity is the unknown intramolecular interaction that can alter both A and GRF values.