The process of tumour invasion and subsequent metastasis represents the most lethal aspect of cancer and is responsible for the majority of deaths among cancer patients. Our objective was to identify invasion-specific genes in a series of isogenic breast cancer cell lines of differing invasive potential using DNA microarray-based transcriptomic profiling. A panel of increasingly invasive breast cancer subclones generated from the primary breast cancer cell line, Hs578T, were subjected to DNA microarray analysis using the Affymetrix HG-U133A array. Data analysis using GeneSpring 6.0 generated a list of 508 differentially expressed genes. A total of 71 genes were down-regulated and 437 genes were up-regulated. Array data for 17 genes was validated using quantitative real-time RT-PCR analysis. A correlation coefficient of 0.9249 was obtained when both technology platforms were compared. Potential new biomarkers for the diagnosis and treatment of invasive breast cancer have been identified.