In　this　paper,　an　ultrasensitive　CE-CL　detection　system　coupled　with　a　novel　double-on-column　coaxial　flow　detection　interface　was　developed　for　the　detection　of　PCR　products.　A　reliable　procedure　based　on　this　system　had　been　demonstrated　for　qualitative　and　quantitative　analysis　of　genetically　modified　organism　-　the　detection　of　Roundup　Ready　Soy　(RRS)　samples　was　presented　as　an　example.　The　promoter,　terminator,　function　and　two　reference　genes　of　RRS　were　amplified　with　multiplex　PCR　simultaneously.　After　that,　the　multiplex　PCR　products　were　labeled　with　acridinium　ester　at　the　5′-terminal　through　an　amino　modification　and　then　analyzed　by　the　proposed　CE-CL　system.　Reproducibility　of　analysis　times　and　peak　heights　for　the　CE-CL　analysis　were　determined　to　be　better　than　0.91　and　3.07%　(RSD,　n　=　15),　respectively,　for　three　consecutive　days.　It　was　shown　that　this　method　could　accurately　and　qualitatively　detect　RRS　standards　and　the　simulative　samples.　The　evaluation　in　terms　of　quantitative　analysis　of　RRS　provided　by　this　new　method　was　confirmed　by　comparing　our　assay　results　with　those　of　the　standard　real-time　quantitative　PCR　(RT-QPCR)　using　SYBR®　Green　I　dyes.　The　results　showed　a　good　coherence　between　the　two　methods.　This　approach　demonstrated　the　possibility　for　accurate　qualitative　and　quantitative　detection　of　GM　plants　in　a　single　run.　©　2008　Wiley-VCH　Verlag　GmbH　&　Co.　KGaA,　Weinheim.