Background: The organisation of junior doctors' work hours has been radically altered following the partial implementation of the European Working Time Directive. Poorly designed shift schedules cause excessive disruption to shift workers' circadian rhythms. Method: Interviews and focus groups were used to explore perceptions among junior doctors and hospital managers regarding the impact of the European Working Time Directive on patient care and doctors' well-being. Results Four main themes were identified. Under "Doctors shift rotas", doctors deliberated the merits and demerits of working seven nights in row. They also discussed the impact on fatigue of long sequences of day shifts. "Education and training" focused on concerns about reduced on-the-job learning opportunities under the new working time arrangements and also about the difficulties of finding time and energy to study. "Work/life balance" reflected the conflict between the positive aspects of working on-call or at night and the impact on life outside work. "Social support structures" focused on the role of morale and team spirit. Good support structures in the work place counteracted and compensated for the effects of negative role stressors, and arduous and unsocial work schedules. Conclusions: The impact of junior doctors' work schedules is influenced by the nature of specific shift sequences, educational considerations, issues of work/ life balance and by social support systems. Poorly designed shift rotas can have negative impacts on junior doctors' professional performance and educational training, with implications for clinical practice, patient care and the welfare of junior doctors.