Abstract A comparative study was undertaken to test the ability of several different topological indices to predict the retention indices of chlorinated benzenes on polar and non-polar stationary phases using both correlation coefficients and correctly predicted elution sequences as criteria of fit. The test was performed on three topological indices: connectivity indices, Wiener numbers, and Balaban indices. The regression analyses showed that the molecular connectivity model predicted the retention indices of chlorinated benzenes more successfully than either Wiener numbers or Balaban indices. The results also demonstrated that the major structural property controlling chromatographic behavior was the size of the chlorinated benzene. In addition, the use of the new non-empirical heteroatom parameterization scheme in the calculation of Wiener numbers and Balaban indices was successfully tested for the first time.