We report the complex cytogenetic analysis of a novel melanoma cell line (M35/01) established from a vertical growth phase of a superficial spreading melanoma. Similarly to its parental tumor, this cell line metastasizes to the liver. Using combined molecular cytogenetic techniques, we could identify a reservoir of chromosomal alterations in M35/01. In addition, we had sufficient amount of DNA from both the original primary tumor and the cell line which allowed for the comparison of their genetic patterns by chromosomal CGH. Several common alterations were found indicating the same clonal origin. These alterations included gains of 6p, 7q, 15q and deletions of 9, 10, 16q and 17p. Chromosomal losses present only in the cell line were detected on chromosome 4, 16p, 18 and gains on 20p12-qter. Array CGH analysis of the M35/01 cell line provided similar results with a much higher resolution, representing relatively high level gains on 7q31.2-q31.31, 15q25, 20q, and losses on 4q28, 9p21-p24, 9q21-q22, 10q25, 16q13-q23, 17p12-13 and 18q12-23. Using SKY-FISH, several structural alterations could be detected which were not recognized by conventional cytogenetics. Except for chromosome 18, none of the centromeres showed normal distribution by FISH. Our analysis shows that a high number of chromosomal alterations, which are known to be nonrandomly associated with melanoma progression, can be found by the combined use of different molecular genetic techniques. This new melanoma cell line would be an excellent model for investigating the mechanism of organ specific-metastatic events of malignant melanoma.