The complexity of public health problems, including the problem of tobacco use behaviors, calls for formal efforts to train transdisciplinary scientists. These scientists can approach problems by using new conceptual frameworks and methodological tools that integrate different disciplinary perspectives. Transdisciplinary training focuses on developing strong scientists with superb core skills while protecting against creating scientists who are "jack of all trades, master of none." Transdisciplinary training is relatively new, with no accepted training model in place. In this paper, we provide a general framework for transdisciplinary training at the advanced graduate and postgraduate levels, with particular reference to tobacco use behaviors. We identify the core attitude, knowledge, and skills competencies that are essential to conducting tobacco use research with a transdisciplinary approach. We outline the structural components of transdisciplinary training that allow for the development of the competencies and discuss what facilitates the transdisciplinary training process. We also discuss the numerous challenges and obstacles to transdisciplinary training. These include the readiness of early-career trainees to undergo transdisciplinary training, professional development risks taken by trainees, administrative and budgetary obstacles inherent in traditional academic institutional structures, and the limited opportunities established scientists have for transitioning their research programs in a transdisciplinary direction. If these obstacles can be overcome, the potential exists for a new generation of transdisciplinary scientists to be trained and be well positioned to make important and unique advances in our understanding of tobacco use and other public health problems.