Abstract Background As the source of a sizeable percentage of research output and the future arbiters of science policy, practice and direction, doctoral (Ph.D.) students represent a key demographic in the biomedical research community. Despite this, doctoral learning in the biomedical sciences has, to date, received little research attention. Methods In the present study we aimed to qualitatively describe the motivational orientations present in semi-structured interview transcripts from a cohort of seventeen biomedical Ph.D. students drawn from two research intensive Australian Group of Eight universities. Results Applying elements of self-determination theory, external and introjected control loci (both strongly associated with alienation, disengagement and poor learning outcomes) were identified as common motivational determinants in this cohort. Conclusions The importance of these findings to doctoral learning is discussed in light of previous research undertaken in higher education settings in the United States and the European Union. With motivation accepted as a malleable, context-sensitive factor, these data provide for both a better understanding of doctoral learning and highlight a potential avenue for future research aimed at improving outcomes and promoting meaningful learning processes in the biomedical doctorate.