The breadth of knowledge required for the multidisciplinary field of nanotechnology challenges and extends traditional concepts of multidisciplinary graduate education. There is a paucity of information, both general reporting and peer-reviewed studies, on the challenges for graduate students working in this multidisciplinary paradigm, from the students’ perspectives. We report two graduate-student perspectives from different instructional models: (i) the core academic department that has expanded student choice by allowing additional classes to be taken from outside the core department and (ii) multiple departments working together to provide choice and diversity across the curriculum. We find, even after many years of multidisciplinary research, that traditional university organizational structure does not easily accommodate multidisciplinary research. In addition, administrative autonomy of academic departments and colleges, competition among various departments for contracts and grant submission, and a disconnect between research and teaching challenge multidisciplinary research endeavors. The students recommend that (i) university administrators support multidisciplinary departments and develop mechanisms to promote faculty participation; (ii) institutions and departments provide more multidisciplinary groups, centers, and institutes and encourage networking through broad collaboration; (iii) more graduate and postdoctoral fellowships for multidisciplinary research be created; and (iv) departments create more flexible curricula allowing their students to participate in more courses outside the department, necessary for a multidisciplinary thesis. Progress in multidisciplinary science will rely both on deep, specialized knowledge and, increasingly, on scientists who can speak a number of scientific languages and take advantage of synergistic connections. As new and more effective approaches to multidisciplinary training are developed, perhaps it is time to listen more to those with the most intimate experience of the system’s successes and failures—the students who are training now to be the next generation of research leaders.