Ductal carcinoma in situ (DCIS) is a heterogeneous group of lesions reflecting the proliferation of malignant cells within the ducts of the breast without invasion through the basement membrane. Numerous studies analyzing the molecular profiles of DCIS using genome-wide unbiased and candidate gene approaches have been conducted with the aim of identifying clinically useful markers that would predict the risk of progression to invasion. Results of these investigations defined the heterogeneity of DCIS at the molecular level, but a gene signature predictive of invasive progression has not been identified. Major diagnostic criteria that differentiate DCIS from invasive cancer are the presence of intact basement membrane and myoepithelial cell layer. Based on this, perturbation of normal myoepithelial cell differentiation has been proposed to explain progression to invasion. Comprehensive molecular studies analyzing large cohorts of DCIS with long-term clinical follow-up are necessary to resolve the many remaining questions.