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Background D3 lymph node dissection is recommended for patients with advanced sigmoid and rectal cancer in Japan. This trial aimed to investigate the feasibility of indocyanine green (ICG) as a tracer to increase the nodal harvest during D3 lymph node dissection in patients with sigmoid and rectal cancer. Methods This prospective randomized clinical trial was performed between May 2021 and April 2022. The inclusion criteria were patients with stage I–III sigmoid or rectal cancer eligible for laparoscopic resection. Patients were 1: 1 randomized to either the ICG group (endoscopic ICG injection at the tumour site and intraoperative imaging to guide dissection) or the control group (routine laparoscopic white-light imaging). All patients were treated with D3 dissection, and the primary outcome was the number of harvested lymph nodes at the D3 level. Results Out of 210 patients screened, a total of 66 patients were enrolled and randomized. Patients in the two groups presented similar ages and clinical stages (ICG group versus control group, median age of 58.0 versus 58.5 years; stage III 36.4 per cent versus 36.4 per cent, whereas the rate of rectal cancer was 27.3 per cent versus 48.5 per cent respectively). ICG imaging was helpful for completely dissecting D3 lymph nodes and could identify a median of more than 2 (range 1–6) D3 lymph nodes neglected by routine laparoscopic white-light imaging during surgery. The median number of D3 lymph nodes harvested in the ICG group was significantly higher than that in the control group (7.0 versus 5.0, P = 0.003); however, there was no significant difference in the median numbers of positive D1, D2, and D3 lymph nodes between the two groups. Conclusion ICG is safe and feasible to guide D3 lymph node dissection and can increase the number of harvested D3 lymph nodes in patients with sigmoid and rectal cancer. Registration number: NCT04848311 (http://www.clinicaltrials.gov).