Based on genetic diversity in the population, there is an expectation, born out by decades of experience, that a given drug or treatment will not be equally efficacious for all patients. While this fact cannot be avoided, with ever increasing knowledge of the drug's biological mechanism of action and the relationship between efficacy and the patient's genetic profile, more directed treatments, with greater potential for efficacy are becoming possible. For example, Herceptin, Genentech's antibody based treatment for HER2 positive metastatic breast cancer, is prescribed based on the results of a diagnostic test, the outcome of which is able to screen out patients who have no chance of responding to the treatment. At the extreme of tailoring medicines to those patients who will receive the greatest benefit, is an autologous, or patient specific approach. Oncophage, a cancer vaccine in late stage clinical trials, is designed to accommodate the unique genetic mutations underlying each patient's cancer. This chapter of the book presents the challenges involved in bringing autologous HSP-based vaccines to commercial reality based on the experiences gained to date in the clinical manufacture of Oncophage. Two guiding principles have dominated our efforts. First, only the product should be autologous. All processes should be standardized to the greatest extent possible. Second, maintaining complete segregation between patient samples at all steps of processing is paramount.