Gene expression patterns as well as gene interactions are under investigation for their involvement in tumour heterogeneity. The molecular classification of breast cancer based on hormone receptor expression, grade and HER2 receptor levels, is indicative but not adequate enough to complete the prognostic data. The objectives of this study were to validate the prognostic value of 19 genes, solely, and as parts of classifiers (sets of genes), in breast cancer patients and to determine whether the expression of these genes and classifiers is correlated with breast cancer molecular classification. Gene expression was examined in the blood of 88 breast cancer patients and 50 healthy controls using multiplex quantitative real-time PCR. Patients with a second primary malignancy showed a statistically significant difference when compared with: i) patients with a single breast cancer, for an 8-gene classifier (p<0.02); and ii) healthy individuals (classifier FBX033, FLJ339115) (p<0.01), with respect to gene expression. The classifier ENY2, USP38 was associated with the development of primary breast cancer. A newly established classifier (ENY2, USP38, RPS7, Osbpl-1 and ETF1) indicated a statistically significant association with HER2 subtype patients, compared to patients with a different molecular classification (p<0.04). The gene FLJ33915 was differentially expressed in a subgroup of HER2-positive patients with infiltrated axillary lymph nodes (p<0.028). We validated the prognostic value of 4 classifiers for primary and second primary malignancy. Evidence of a classifier predicting the HER2 subtype and the gene FLJ33915 which subdivides HER2 subtype patients is also presented.