A case of primary intrahepatic sclerosing cholangitis associated with inflammatory bowel disease, which is rare in Japan, is reported. A 16-year-old Japanese boy was admitted to our hospital because of abdominal pain and fever. He was diagnosed as having primary intrahepatic sclerosing cholangitis by endoscopic retrograde cholangiography and liver biopsy. Inflammatory bowel disease was diagnosed by colonoscopy and biopsy of the colonic mucosa. Human lymphocyte antigen typing showed HLA-A2, A-9, -B52 and -DR2.