Advances in high-throughput technology and bioinformatics have made it possible to analyze tumors in an unbiased manner at the genomic level. These techniques aim to produce novel prognostic and predictive biomarkers, and most importantly, mechanistic insights that can be translated into ground-breaking therapeutic hypotheses. Genome-wide analysis is particularly relevant to the study of triple negative breast cancer (TNBC), as effective targeted therapy would make a considerable impact. At the transcriptome level, TNBC most frequently overlaps the intrinsic subtype referred to as "Basal-like''. However other less common subtypes, including "Claudin-low", "HER2-enriched but without HER2 gene amplification", "Luminal B", "Luminal A" and "Molecular apocrine'' subtypes have also been described in TNBC. Additionally TNBC tumors that arise in the setting of a germ-line BRCA1 mutation may be considered a separate entity because of their potential susceptibility to poly ADP ribose polymerase (PARP) inhibitor therapy. With the advent of whole genome sequencing, we envision further classification of TNBC that is based on genetic abnormalities linked to targeted therapeutics.