Only a few reports exist of cytogenetic studies in nasopharyngeal carcinoma (NPC), probably because of the technical limitations of culturing solid tumors. We established a cell line (cell-666) that was derived from an NPC xenograft growing in athymic nude mice. Epstein-Barr virus (EBV) infection is one of the important etiologic factors of NPC. This cell line has been shown to have the consistent presence of EBV by Epstein-Barr virus encoded RNAs (EBER) in situ hybridization. Furthermore, aberrant methylation of 5'CpG island of p16 gene was detected. Thus, this cell line represents a valuable model for the study of NPC tumorigenecity. The karyotype of this newly established cell line is: 45,X,del(X)(q24),-5der(5)(5pter-->5q31::5q13-->+ ++5q31::5p12-->5pter),der(6;?) (q10;p10),add(7)(p22), + 9, del(11)(q13),add(12)(p13),-14,-18,-21, + 2mar. Fluorescence in situ hybridization analyses were performed using whole chromosome painting probes of chromosomes 5, 6, 11, and 12.