Polychlorinated naphthalenes (PCNs) and chlorinated paraffins (CPs) are the groups of persistent organic pollutants (POPs) prone to the long-range atmospheric transport and deposition. The global extent of the POP pollution became apparent when they were detected in the areas, where they have never been used or produced at levels posing risks to the wildlife. Both PCNs and CPs are persistent, and they can be accumulated in the living organisms. PCNs are more or less planar, and several investigated congeners exhibited a high dioxin-like toxicity. Short chain chlorinated paraffins were classified as the Category 3 carcinogens. PCNs and CPs have been detected in a wide range of environmental compartments. New fractionation method enabling the simultaneous determination of polychlorinated biphenyls, organochlorinated pesticides, polychlorinated naphthalenes, and chlorinated paraffins is presented here. This method was applied in the study focused on contamination of the air and soil in the Czech Republic by less frequent types of persistent substances. Recent data about the PCN and CP contamination of this region is presented here.