BACKGROUND Antiviral therapy for chronic hepatitis C may cause transient on-treatment response followed by post-treatment relapse. OBJECTIVES We have compared the prognostic value for post-treatment relapse of minimal hepatitis C residual viraemia detected at end-of-therapy by transcription mediated assay (TMA) and by Abbott RealTime PCR HCV assay. STUDY DESIGN Minimal residual viraemia was investigated in 202 HCV patients who had completed a full course of Pegylated Interferon (PEG-IFN) plus ribavirin and were HCV-RNA negative by conventional PCR in two separate serum samples obtained during the last week of therapy and the results were then correlated with post-treatment outcome. RESULTS Minimal residual viraemia was detected in 22/202 (11%, 95% CI: 7-16%) and in 28/202 (13.8%, 95% CI 10-19%) patients by TMA and by Abbott RealTime HCV assay, respectively, with 92% concordant results. Post-treatment relapse was seen in 81.8% (95% CI: 60-93%) of TMA positive and in 82.1% (95% CI: 64-92%) of Abbott RealTime HCV assay positive cases compared to 16.6% (95% CI: 12-23%) of TMA negative and 17.2% (95% CI: 12-23%) of Abbott RealTime HCV assay negative patients. CONCLUSIONS These results indicate that TMA and the Abbott RealTime HCV assay have comparable sensitivity and specificity in identifying minimal residual viraemia at the end of antiviral therapy, with excellent predictive value for post-treatment relapse.