Vinblastine (VBL) is used to treat certain kinds of cancer including Hodgkin's lymphoma, lung cancer, breast cancer, testicular cancer and cervical carcinoma. However, the rapid development of resistance during therapy remains a major clinical challenge. In order to reverse cancer cell resistance, the goal of this study was to find differentially expressed genes and chromosomal alterations in multidrug resistant (MDR) KB-v1 cells, further to probe the relationship between drug resistance and differential genes, and chromosomal changes in MDR cancer cells. Comparative genomic hybridization (CGH) analysis of MDR KB-v1 and their parental KB-3-1 cells revealed chromosomal changes; microarray-based expression profiling was carried out by comparing the gene expressions of MDR KB-v1 cells and KB-3-1 cells. We have identified 3 chromosomal gains in regions of 1p31, 7q21 and 18q21 in MDR cells and 10 genes (CYR61, UGTREL7, MBD1, NARS, ATP5A1, ABCB1, ABCB4, PEG10, MCM7, SERPINE1) contained in these regions were also up-regulated in MDR KB-v1 cells. Forty-nine genes were down-regulated when KB-v1 cells were subjected to lower dose or depletion of the drug. We have confirmed some gene expression changes by reverse transcription-polymerase chain reaction and Northern blots. These are the first data describing the relationship of 1p31 and 18q21 chromosomal aberrations and candidate genes in acquired vinblastine-resistance. This study also demonstrates that the combination of CGH and cDNA microarray is a very useful tool to detect drug resistant targets in cancer treatment.