BACKGROUND: In 2004, the Malawian Ministry of Health declared a human resource crisis and launched a six year Emergency Human Resources Programme. This included salary supplements for key health workers and a tripling of doctors in training. By 2010, the number of medical graduates had doubled and significantly more doctors were working in rural district hospitals. Yet there has been little research into the views of this next generation of doctors in Malawi, who are crucial to the continuing success of the programme. The aim of this study was to explore the factors influencing the career plans of medical students and recent graduates with regard to four policy-relevant aspects: emigration outside Malawi; working at district level; private sector employment and postgraduate specialisation. METHODS: Twelve semi-structured interviews were conducted with fourth year medical students and first year graduates, recruited through purposive and snowball sampling. Key informant interviews were also carried out with medical school faculty. Recordings were transcribed and analysed using a framework approach. RESULTS: Opportunities for postgraduate training emerged as the most important factor in participants' career choices, with specialisation seen as vital to career progression. All participants intended to work in Malawi in the long term, after a period of time outside the country. For nearly all participants, this was in the pursuit of postgraduate study rather than higher salaries. In general, medical students and young doctors were enthusiastic about working at district level, although this is curtailed by their desire for specialist training and frustration with resource shortages. There is currently little intention to move into the private sector. CONCLUSIONS: Future resourcing of postgraduate training opportunities is crucial to preventing emigration as graduate numbers increase. The lesser importance put on salary by younger doctors may be an indicator of the success of salary supplements. In order to retain doctors at district levels for longer, consideration should be given to the introduction of general practice/family medicine as a specialty. Returning specialists should be encouraged to engage with younger colleagues as role models and mentors.