BACKGROUND: Neoadjuvant chemoradiotherapy (nCRT) is the standard for locally advanced rectal cancer (LARC). However, distant metastasis remains the primary cause of treatment failure. Early identification of high-risk individuals for personalized treatment may offer a solution. Circulating tumour DNA (ctDNA) could assist in this process. METHODS: From September 2017 to June 2019, the study prospectively recruited 113 patients with LARC (cT3-4N0M0 or cTanyN + M0) who underwent nCRT followed by radical surgery across 8 tertiary centers. ctDNA was analysed using large-panel targeted sequencing at baseline, during nCRT, pre-surgery, post-surgery, post-adjuvant chemotherapy (ACT), and during annual follow-ups for 3 years. FINDINGS: We analysed 103 tissue and 669 plasma samples from 103 patients. With a median 53-month follow-up, significantly worse progression-free survival (PFS) and overall survival (OS) were observed if median variant allele frequency (mVAF) of baseline ctDNA per patient was ≥0.5% (PFS, HR 4.39, p <
0.001
OS, HR 5.61, p = 0.004) or ctDNA was still detectable two weeks into nCRT (PFS, HR 7.63, p <
0.001
OS, HR 5.08, p <
0.001). Furthermore, when compared to the low-risk (C1) group (characterized by "ctDNA undetected during nCRT with baseline mVAF <
0.5%" or "ctDNA undetected during nCRT with TMB (tumour mutational burden) ≥20/Mb"), the high-risk (C2) group (characterized by "ctDNA detected during nCRT" or "baseline mVAF ≥0.5% with TMB <
20/Mb") showed significantly worse long-term outcomes (3 y-PFS, 55.9% vs. 94.2%
3 y-OS, 79.4% vs. 100%). The ctDNA clearance during nCRT, baseline mVAF, and TMB may be effective prognostic indicators. INTERPRETATION: Our findings reaffirm the clinical monitoring value of ctDNA and demonstrate the strong prognostic value of baseline ctDNA and its early clearance status in patients with LARC undergoing nCRT. This highlights the potential of dynamic ctDNA monitoring as actionable stratified indicators to guide personalized neoadjuvant treatment strategies. FUNDING: This work was supported by the Major Grants Program of Beijing Science and Technology Commission (No. D171100002617003) and the National High Level Hospital Clinical Research Funding (2022-PUMCH-C-005).