This chapter addresses general Phase II clinical development issues and pitfalls and the relationship of Phase II to the preceding and subsequent phases of development, and then focuses on the new issues introduced into Phase II development by the emergence of personalized medicine. The dosing frequency to test should be derived from preclinical data and from human biomarker evidence of the development of and recovery from tolerance to intended effect. Indication selection, matching targets to patients, can be facilitated by collecting appropriate genetic or other biological information about the proposed subject population, and assuring that the biology of the subjects is matched to the drug candidate's proposed mechanism. Biomarker technologies have proven their mettle in a number of applications, and practical methods are now available that enable the drug development process. CNS drug developers and their development plans need to adapt to incorporate the changes brought by personalized medicines.