Array comparative genomic hybridization (aCGH) is a key platform to assess cancer genomic profiles. Many structural genomic aberrations cannot be detected by aCGH alone. We have applied molecular cytogenetic analyses including spectral karyotyping, multicolor banding, and fluorescence in situ hybridization with aCGH to comprehensively investigate the genomic aberrations associated with cisplatin resistance in A2780 ovarian cancer cells. A2780 is a well-established model of chemotherapeutic resistance with distinct karyotypic abnormalities in the parental and cisplatin-resistant cells. Cytogenetic analysis revealed that two unbalanced translocations, der(8)t(1;8) and der(X)t(X;1), and loss of chromosome 13 were present only in the resistant line. Our aCGH analyses detected imbalances affecting an additional 10.59% of the genome in the cisplatin-resistant cells compared with the parental. DNA copy number changes included deletions at 1p10–p22.1, 8p23.3, and Xq13.1-pter, and a duplication of 8q11.22-q23. Cryptic genomic aberrations associated with concurrent localized changes of specific gene expression included a homozygous deletion of 0.38 Mb at 1p21.3 adjacent to SNX7, and an insertional transposition of 0.85 Mb from 13q12.12 into chromosome 22. This latter rearrangement led to an overexpression of four contiguous genes that flanked one of the breakpoint regions in chromosome 13. Furthermore, 17 genes showed differential expression correlating with genomic gain or loss between the resistant and parent lines, validated by a second expression array platform. These results highlight the integration of comprehensive profiling to determine relationships of genomic aberrations and genes associated with an in vitro drug resistance model in ovarian cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. © 2008 Wiley-Liss, Inc.