Background/aims: Carcinogenesis of intrahepatic cholangiocarcinoma (ICC)-associated liver fluke infection accumulated genetic and epigenetic alterations. Cholangiocarcinoma cell line (KKU-M213) is adenosquamous carcinoma which rare variants and not commonly found in ICC. However, interactions of liver fluke-associated ICC proceed to genetic alterations in adenosquamous carcinoma that have been not elucidated. Objectives: To analyze the whole genome-wide genetic alterations in KKU-M213 using microarray comparative genomic hybridization. Methods: DNA of KKU-M213 and matched-sex reference were differentially labeled with fluorescence dries (Cy3 and Cy5) and mixed together with cot-1 DNA. The mixture was hybridized on array with spotting 2,464 human bacterial artificial chromosomal (BAC) clones in triplicate and mapped these directly onto human genome sequence. The genetic alterations were classified the DNA copy-number variations according to the intensities of log2 ratio (Cy3/Cy5) as DNA copy-number loss/gain and deletion/amplification. Results: the whole genomic alterations in KKU-M213, which revealed a variety of chromosomal aberrations with a part and/or entire chromosomal gain and loss. Chromosomal amplifications were detected on 4q13.1, 4q21.1, 4q21.2, 5p tel, and 5p15.3, whereas homozygous deletions were detected on 1q23, 1q25, 1q31, 1q32-41, 1q32.2, 1q41, 1q43, 5q15-5q21, 8p22-8p23, 9p24, 10q11.2, 10q11.2-10q2.1, 10q11.2, 10q21.1 and 20q13.3. Conclusions: The whole genome-wide genetic alterations were characterized which previously not defined in adenosquamous carcinoma. This recent advance tool is usefulness for discovering novel cancer-related gene (oncogene/tumor suppressor gene) and substitutes in in vivo experiment for functional testing of candidate gene involving liver fluke-associated ICC carcinogenesis.