Recent reports show that phase I trials are increasingly including dose expansion cohorts, after the maximum tolerated dose (MTD) has been reached, in order to better characterize the toxicity profile. In addition, expansion cohorts are frequently used to seek early signs of efficacy within a specific disease population or to evaluate other endpoints. In this presentation we will discuss the aims of phase I trials with expansion cohorts (and possibly Ph I/II trials) and provide a link between the aims, designs, and methods of analysis. We will illustrate how to carry out a complete analysis using information from all patients. The proposed methods are evaluated through simulations. An example of an application to an ovarian vaccine clinical trial will also be discussed. This is joint work with John O’Quigley.