To evaluate the risk factors and long-term prognosis of metachronous rectal cancer in the remnant rectum of patients with familial adenomatous polyposis (FAP). Sixty-five patients (49 families) who underwent prophylactic surgery, including bowel resection, for FAP between January 1976 and August 2022 at Hamamatsu University Hospital were included and divided into two groups based on the presence of metachronous rectal cancer. Risk factors for metachronous rectal cancer development were analysed in cases treated with total colectomy with ileorectal anastomosis (IRA) and stapled total proctocolectomy with ileal pouch anal anastomosis (IPAA) (IRA, n=22; stapled IPAA n=20; total, n=42). The median surveillance period was 169 months. Twelve patients developed metachronous rectal cancer (IRA, n=5; stapled IPAA, n=7), of which six with advanced cancer died. Patients who temporarily dropped out of surveillance were significantly more likely to have metachronous rectal cancer (metachronous vs. non-metachronous rectal cancer: 33.3% vs. 1.9%, p<0.01). The mean duration of surveillance suspension was 87.8 months. Cox regression analysis revealed that temporary surveillance drop-out independently affected the risk (p=0.04). The overall survival associated with metachronous rectal cancer was 83.3% at 1 year and 41.7% at 5 years. Overall survival was significantly worse in advanced cancer than in early cancer cases (p<0.01). Temporary drop-out from surveillance was a risk factor for metachronous rectal cancer development, and advanced cancer had a poor prognosis. Continuous surveillance of patients with FAP, without temporary drop-out, is strongly recommended.