Objective To investigate the molecular events and metastasis-related genes in ACC-2 and ACC-M cells of adenoid cystic carcinoma. Methods Adenoid cystic carcinoma cell line ACC-2 and a sample of adenoic cystic carcinoma cell clones highly metastatic to the lung (ACC-M) were investigated. ACC-2 and ACC-M cells were cultured and collected. Total RNA was extracted using standard Trizol RNA isolation protocol. The poly A mRNA was purified and labeled in reverse transcription using M-MLV reverse transcriptase in the presence of Easytides deoxyadenosin 5 triphosphate [alpha-33 p]. A cDNA array was assembled with 7675 EST clones which represented the same number of independent single genes. Prepared nylon membranes were hybridized with the [alpha 33p]-dATP labeled mRNA from ACC-2 and ACC-M cells. Membranes were exposed to phosphor screen. Results The high-through put analysis of gene expression pattern was obtained from ACC-2 and ACC-M cells by the hybridization of the cDNA array. The difference of parallel gene expression was analyzed. Genes were clustered according to their expression level in the ACC-M compared with ACC-2 cells. According to each genes ratio of expression level, there were 17 genes which were upregulated with ratios over 3.0, and there were 12 genes which were downregulated with ratios below 0.33 (1/3.0=0.33). Conclusions Significantly different expression patterns between ACC-2 and ACC-M by cDNA array were observed. The differences lie in signal pathways, tumor antigens, immune molecular and some unknown genes.