Measurement of toxicologically relevant polychlorinated biphenyl (PCB) congeners such as non-ortho(IUPAC#) 77, 81, 126, 169 and mono-ortho 105, 114, 118, 123, 156, 157, 189 and di-ortho 170, 180 and polybrominated diphenyl ethers (PBDEs) such as 47, 66, 85, 99, 100, 138, 153, 154 in environmental samples become almost mandatory in several countries now. However, most of the available methods involve expensive instrumentations such as HRGC-HRMS or ECNI-LRMS, apart from expensive extraction and clean-up (with large volume of solvents) steps. A method has been devised combining the analytical separation power of PYE [2-(1-pyrenyl)ethyldimethysilylated silica] column HPLC and high-resolution gas chromatographic techniques including micro-electron capture detection (ECD) and two dimensional gas chromatograpy-ECD techniques to determine these eco-toxic substances at parts-per-trillion (ppt) levels. This combination resolves co-elution of congeners that occur in disproportionate ratios (e.g. CB-110 and -77) and allows accurate congener-specific determination of target compounds. This method is cost effective as it requires only hexane, that in small quantities (10 mL) and GC-ECD. The elution and analysis time are optimized to less man hours. This method is effectively utilized in the analysis of co-planar PCBs and PBDEs from archived solvent extracts of samples previously analyzed for pesticides and PCBs. Structure based separation of contaminant classes improves GCECD determination at ppt levels.