Breast cancer is considered to be a multifactorial disorder caused by both genetic and non-genetic factors. Different histological types of breast cancer differ in response to treatment and may have a divergent clinical course. Breast tissue is heterogeneous, with components of epithelial, mesenchymal, endothelial and lymphopoietic derivation. The genetic heterogeneity of invasive breast cancer is reflected by the wide spectrum of histological types and differentiation grades. Nevertheless, the influences of these cell types on the tumour's total pattern of gene expression can be estimated analytically. Microarrays permit total tissue analysis and provide a stable molecular portrait of tumours. Some investigations suggest differences in the gene expression profiling for ductal and lobular carcinomas. It has been reported that inactivating mutations of the E-cadherin gene are very frequent in infiltrating lobular breast carcinomas. Other than altered expression of E-cadherin, little is known about the underlying biology that distinguishes ductal and lobular tumour subtypes. However, about 8 genes have been identified differentially which are expressed in lobular and ductal cancers: E-CD, survivin, cathepsin B, TPI1, SPRY1, SCYA14, TFAP2B, and thrombospondin 4, osteopontin, HLA-G, and CHC1. Expression profiling of breast cancers can be used diagnostically to distinguish individual histologic subclassifications and may guide the selection of target therapeutics. However, future approaches will need to include methods for high throughput clinical validation and the ability to analyze microscopic samples.