There is a continued interest in the development of new on-chip protocols for the determination of the causes of infectious disease. In this paper, we demonstrate the use of surface-enhanced resonance Raman scattering (SERRS) for detecting the clinically relevant nucleic acid sequences of Chlamydia trachomatis in a bead-based lab-on-a-chip format, incorporating a solid-phase sample clean-up on-chip. The assay uses streptavidinated polymer microspheres to capture a biotinylated PCR product of the oligonucleotide sequence, which was subsequently hybridized against a complementary rhodamine-labeled, Raman active probe. Central to the assay is an in-channel integrated microfilter, which was used to retain the microspheres, enabling the bound target to be separated from the rest of the sample as part of a solid-phase clean-up (thereby removing any contributions from the background). After washing, the bound Rhodamine labeled detection probe was released thermally from the microspheres by heating and was subsequently mixed on-chip with a stream of silver nanoparticles. The signal was detected downstream using a Raman spectrometer to collect the SERRS response. The assay offers several advantages over traditional laboratory methods, including: the speed of the assay on-chip, the potential for sample clean-up; and the low volume of sample required.