The retention of organochlorinated compounds on an immunochromatographic column is studied. The compounds considered are usually found together in real samples of environmental concern, and include chlorinated biphenyls, chlorinated dibenzo-p-dioxins, chlorinated dibenzofurans, and organochlorinated insecticides. The different retention observed for different compounds is interpreted in light of the structural similarities of the compound studied with that used as a hapten to raise the antibodies employed as ligands in the immunochromatographic column. Differences in retention of the organochlorinated compounds on the immunocolumn make it possible to fractionate them. Mixtures of phosphate buffer solution and ACN in different ratios were used as desorption agents. Depending on the percentage of ACN employed, different fractionations of the organochlorinated compounds are obtained. The use of 20% ACN allows fractionation of most insecticides from chlorinated biphenyls, dioxins, and furans. Besides, chlorinated biphenyls of different chlorination degree can be separated. Moreover, pentachlorinated dioxins and pentachlorinated furans are separated from hexachlorinated biphenyls. Fractionation is of critical importance from a practical point of view, as it avoids some of the interferences that otherwise take place during the subsequent gas chromatography/mass spectrometry (GC/MS) analysis of these compounds. In this way, immunochromatography makes it possible to perform in a single step all the processes (extraction, clean-up, concentration, and fractionation) that are needed prior to the GC/MS analysis of these analytes in aqueous samples. An additional advantage of this method is the reusability of the immunoaffinity chromatography column for more than 500 times.