Each normal organ and pathological condition expresses a distinct set of molecules on their vasculature. These molecular signatures have been efficiently profiled using in vivo phage display. Several peptides homing to tumor blood vessels, lymphatic vessels, and/or tumor cells as well as to various normal organs have been isolated using this method. The in vivo screening of phage libraries has also revealed novel tissue-specific biomarkers of the normal and diseased vasculature. Tumor-homing peptides have been successfully used to target therapeutics and imaging agents to tumors. In vivo phage display has also been used in the identification of cell and/or tumor type-specific cell-penetrating peptides, which further facilitate the transmembrane delivery of various cargo molecules into cells. In this review we describe experimental setup for a combined ex vivo and in vivo screening procedure to select both conventional and cell-penetrating peptides homing to brain tumors.