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Background Previous studies reported that nephrotic syndrome is associated with ulcerative colitis (UC) patients treated with mesalazine. Dysplasia associated with UC often develops into colorectal carcinoma. Case presentation A 17-year-old man was referred to our hospital, complaining of diarrhea and bloody stool. Total colonoscopy (TC) was performed and total-type UC was diagnosed. After treatment with mesalazine for 5 years, a low-grade dysplasia (LGD) was detected in the rectum by histological analysis of a biopsy sample. One month later, he complained of dyspnea and edema. He was diagnosed with nephrotic syndrome and administered steroid and immunosuppressant treatment: cyclosporine and mizoribine. Eight years after LGD was detected, he complained of abdominal distension and pain. Stenosis of the upper rectum by an advanced rectal carcinoma was detected. Abdominal computed tomography showed a rectal tumor with multiple lymph node metastases. Transverse colostomy was performed surgically, followed by two cycles of modified FOLFOX6 and panitumumab. He safely underwent a total proctocolectomy with a stapled ileal pouch anal-canal anastomosis, total mesorectal and bilateral pelvic lymph node dissection, and temporary loop ileostomy. Metastases were observed in 25 lymph nodes microscopically. The pathological stage of rectal carcinoma was pT3N2bM1a. After one cycle of modified FOLFOX6 postoperatively, he was discharged from the hospital. Conclusions A patient with UC associated with nephrotic syndrome was treated with mesalazine. LGD developed into an advanced rectal carcinoma after an 8-year interval. The use of immunosuppressants for the treatment of nephrotic syndrome might affect the development of rectal carcinoma. Trial registration Trial registration: Case report registration #1626