Despite recent improvements in the breast cancer mortality rate, breast cancer remains the most common cancer and the second leading cause of cancer-related deaths in US women. A decreasing trend in mortality rates is caused by advances in early detection and, to a lesser degree, in cancer therapies. With the increased utilization of mammography, one of the earliest detectable breast tumors, ductal carcinoma in situ, has become the most rapidly increasing subset of breast cancers. Contrary to the dramatic improvement in our ability to detect ductal carcinoma in situ, the pathophysiology of this disease is still poorly understood. Many molecular studies have been performed in ductal carcinoma in situ lesions with the aims of identifying genes involved in breast cancer initiation and progression, defining the relation between in situ and invasive carcinomas, and identifying clinically useful markers for breast cancer diagnosis, prognostication, prevention, and treatment.