To facilitate the study of the mechanisms of breast cancer metastasis we have previously characterized a pair of breast tumor cell lines that originate from the same breast tumor cell line MDA-MB-435, but which have diametrically opposite metastatic capabilities. These cell lines constitute a stable and accessible experimental system for the identification of metastasis-related genes and for the study of their role in the process of metastasis. In this study, we used a combination of RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) fingerprinting and cDNA arrays (here termed "RAP-array") to identify genes differentially expressed with respect to metastatic phenotype. RAP-PCR was used to generate radioactive probes of reduced complexity for hybridization to nylon membranes containing 588 cDNAs of known identity. Single RAP-PCR fingerprint probes hybridized from 61 (10.4%) to 116 (19.7%) of the filter array targets, with a signal detection overlap of approximately 21%. A total of 344 (57%) of the 588 target genes were detected by five single RAP-PCR fingerprints. The advantage of using reduced complexity probes was highlighted by the fact that the combination of RAP probes before hybridization compromised the overall detection rate by up to 40%. Sequential application of RAP-PCR probes allowed the screening of a greater, and an alternative fraction of the transcript population than was achieved with a radiolabeled total cDNA probe. Verification by quantitative reverse transcriptase-PCR confirmed significantly increased expression of keratin 9 (>100-fold) in nonmetastatic breast tumor cells and of CD70 (fivefold) in metastatic cells. The differential expression of keratin 9 and CD70 was maintained between cells grown as primary xenografts in athymic mice. The RAP-array method enabled the detection of genes not revealed using other screening methods and that are candidates for further investigation in the context of metastatic phenotype.