Objectives: To examine the extent, and nature, of impact on junior doctors’ career decisions, of a proposed new contract and the uncertainty surrounding it. Design: Mixed methods. Online survey exploring: doctors’ future training intentions; their preferred specialty training (ST) programmes; whether they intended to proceed immediately to ST; and other plans. Linked qualitative interviews to explore more fully how and why decisions were affected. Setting: Doctors (F2s) in second year of Foundation School (FS) Programmes in England. Participants: Invitations sent by FSs. Open to all F2s November 2015 – February 2016. All FSs represented. Survey completed by 816 F2s. Sample characteristics broadly similar to national F2 cohort. Main outcome measures: Proportions of doctors intending to proceed to ST posts in the UK, to defer or to exit UK medicine. Proportion of doctors indicating changes in training and career plans as a result of the contract and/or resulting uncertainty. Distribution of changes across training programmes. Explanations of these intentions from interviews and free text comments. Results: Among the responding junior doctors, 20% indicated that issues related to the contract had prompted them to switch specialty and a further 20% had become uncertain about switching specialty. Switching specialty choice was more prevalent among those now choosing a community-based, rather than hospital-based specialty. 30% selecting general practice had switched choice because of the new contract. Interview data suggests that doctors felt they had become less valued or appreciated in the National Health Service and in society more broadly. Conclusions: Doctors reported that contract-related issues have affected their career plans. The most notable effect is a move away from acute to community-based specialities, with the former perceived as more negatively affected by the proposed changes. It is concerning that young doctors feel undervalued, and this requires further investigation.