Presented herein is a rare case of invasive biliary cystic tumor without an ovarian-like stroma, and the apparent sequence underlying its malignant transformation, which was identified on detailed histological examination. A 54-year-old woman was incidentally diagnosed as having a cystic tumor in segment VIII of the liver, and central bisegmentectomy was performed. Macroscopically the tumor measured 4.6 x 3.5 cm; and unilocular cystic and solid areas were seen on cut surface. Microscopically the tumor showed three types of neoplasia: adenoma and tubulopapillary adenocarcinoma in the cystic area, and invasive adenocarcinoma in the solid area. The relative area of the tumor occupied by each of these histological types was approximately 3%, 50% and 47%, respectively. Moreover, transitional zones between adenoma and tubulopapillary adenocarcinoma, and between tubulopapillary adenocarcinoma and invasive adenocarcinoma were noted. The immunohistochemical expression of Ki-67 and p53 increased gradually from adenoma through to tubulopapillary adenocarcinoma, and was highest in invasive adenocarcinoma. MUC1 was positive, and MUC2 and MUC5AC were both negative. No ovarian-like stroma or communication with the bile ducts around the tumor was found in any area of the specimen. On the basis of the World Health Organization histological classification and these pathological findings, the present case was diagnosed as invasive-type biliary cystadenocarcinoma.