The analysis of recurring chromosome aberrations has become an integral part of the diagnostic and prognostic workup of many human cancers, and their molecular analyses have facilitated the identification of genes related to the pathogenesis of cancer. Cholangiocarcinoma (CC), a malignant neoplasm of the biliary epithelium, is usually fatal because of the difficulty in early diagnosis and unavailability of effective therapy. Furthermore, little is known about the genetics and biology of CC. Only few reports concerning cytogenetic studies of CC have been published and few cell lines have been established. We recently established CC cell line, designated as PCK1. The purpose of this study is to establish in detail karyotype of PCK1 cell line. The origins of the unidentified marker chromosomes were analyzed by G-banding, cross species color banding (RxFISH), and human chromosome-specific painting. In PCK1 cell line, gains involved chromosomes and chromosome regions, 4, 5, 9, 12, 16, 21, 1q, 7q11-q22, 8q, 12p, 14q11-q22, 15q21-qter, 17p11-qter, and 18p. Losses involved Y, 7q31-qter, 8p, 14q23-qter, 17p12-pter, and 18q. Established PCK1 cell line will be able to use the basic research of cholangiocarcinoma and the abnormal chromo-somes may be the candidate regions for isolation of the genes related to CC.