Anthocyanin pigments are extracted from various plants and used for diverse purposes. The overall goal of this study was to develop high-anthocyanin corn to enhance the economic efficiency of anthocyanin production. We determined and compared the anthocyanin contents from the different parts of purple corn in various breeding lines. Our results revealed that purple corn produced the anthocyanin pigment throughout the plant, especially high in the husk and cob regions, although anthocyanin levels varied significantly among different plant parts. We analyzed the 295 selected lines from the 2006 breeding population, and it showed that anthocyanin levels of husks ranged from 17.3% to 18.9% of dry weight, roughly 10 times more than the standard current purple corn kernel content, 1.78%. LC-MS/MS analysis demonstrated that the main components of purple corn husk anthocyanin were cyanidin derivatives, and the most prevalent constituents were cyanidin-3-glucoside, cyanidin-3-succinylglucoside and pelargonidin-3-(6''-malonylglucoside). The results suggested that high-anthocyanin corn will boost the purple corn pigment production far more than its current level.