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Although no optimal treatment is currently available for malignant brain tumors, as the molecular mechanisms underlying brain tumor development have been delineated, new chemotherapeutic agents that act directly on specific molecular targets have become available. Defining a specific molecular target raises the possibility that the molecular effects of a given agent can be analyzed in patients in a clinical trial. Specifically, whereas standard phase I and II clinical trials classically determine the safety and efficacy of agents by using indirect global end points, these new biological agents afford the opportunity to incorporate molecular end points into phase I and II clinical trials to determine whether the agent under investigation is actually doing what it was intended to do. This work presents avenues for improving current brain tumor clinical trial designs based on the molecular specificity of new agents and the unique features of brain tumors. Specifically, the authors recommend brain-applicable phase I and II clinical trial strategies that take advantage of the targeted nature of new agents to maximize information about their efficacy, toxicity, and molecular effects.