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A molecular electronegativity distance vector based on 13 atomic types (MEDV-13) is used to describe the structures of 62 polychlorinated naphthalene (PCN) congeners and related to the gas chromatographic relative retention indices (RIs) of PCNs. Using multiple linear regression, a 4-variable quantitative structure(retention relationship (QSRR) with the correlation coefficient of estimations (r) being 0.9912 and the root mean square error of estimations (RMSEE) being 31.4 and the correlation coefficient of predictions (q) and the root mean square error of predictions (RMSEP) in the leave-one-out procedure are 0.9898 and 33.76, respectively.