Research in psychoanalysis is in many ways dependent on some level of engagement with patients in ongoing treatments. The use of patients as study participants may complicate the process of research as well as affect treatment outcomes, and, thus, requires that researchers and clinicians give careful thought to the ways in which they involve patients in research. This article discusses the impact that empirical study may have on the treatment, both positive and negative, while also keeping in mind the ethical issues raised by engaging active patients in research. The importance of balancing research design with patient experience is carefully considered, and suggestions are offered for designing studies that may minimize the potential for negative impact while maintaining the treatment enhancing aspects of research.