The training of transdisciplinary science is distinct in its intention to develop scientists who synthesize the theoretical and methodologic approaches of different disciplines. As a result, transdisciplinary scientists are better prepared to address the complexities of health problems. The most common form of transdisciplinary training is the multi-mentor apprenticeship model, with each mentor training from his or her own discipline. The transdisciplinary trainee is faced with many challenges, including learning the languages and cultures of different disciplines along with learning how to navigate within and between disciplines. The trainee also confronts unique career development risks. The climb up the academic ladder can be slower, rougher, and less linear than that of the trainee's single-disciplinary-trained peers. A number of factors can help the trainee in overcoming the challenges: being able to develop a core set of values and behaviors that are essential for transdisciplinary scientists; having the commitment and support of training institutions, training directors, and mentors; and having training structures and processes in place to prevent the training and trainee from naturally regressing back to familiar single-disciplinary approaches. There is relatively little known empirically about transdisciplinary training. Future efforts can focus on developing a better understanding of the unique characteristics of transdisciplinary training, identifying the effective elements that relate to training outcomes, defining the critical outcome metrics at different time points during and following training, and creating toolkits to help with training processes.