BACKGROUND In preparation to work as junior doctors (JD), University of Auckland final year medical students (FYMS) work as apprentices attached to hospital teams and general practices. Because of anecdotal evidence of student stress, a shortened academic year was introduced in 2007 (42 instead of 47 weeks). OBJECTIVE To determine FYMS perceptions of the final-year medical course and whether or not these perceptions changed in the cohort undergoing a shortened academic year. METHODS All 2006 FYMS completing a 47-week year, and all 2007 FYMS completing a shortened 42-week year, were invited to complete a questionnaire on the final academic day. RESULTS 116/136 (85.3%) and 118/132 (89.4%) of FYMS completed the questionnaire in the 2006 and 2007 cohorts respectively. Significantly fewer students in the 2007 cohort perceived that the year was "a little too long" (10.1% vs 24%, p=0.001), however this did not alter reported stress levels. The mean (-/+SD) Perceived Stress Scale's were 21.7-/+7.0 (2006) and 21.2-/+7.4 (2007), which are similar to the general population (19.6-/+7.5, range 0-45). Visual analog ratings (0-100) showed FYMS felt the programme was enjoyable 72.4-/+18.1, 73.9-/+17.9, despite feeling a degree of pressure 51.2-/+21.3, 47.19-/+20.31 and fatigue 51.4-/+20.3, 53.2-/+21.3. FYMS were largely happy with their decision to become doctors 75.9-/+18.5, 76.2-/+21.1 and felt mostly prepared 60.6-/+18.7, 62.3-/+20.8 but anxious 63.1-/+23.5, 57.7-/+24.4 about working as a JD the following year (all p<0.05). 76% and 73% of the 2006 and 2007 cohort reported being at least adequately prepared for their first house officer role (visual analogue score =50). Both the 2006 and 2007 cohorts considered their elective, general medical, general surgical, and radiology attachments of greatest use. CONCLUSIONS Shortening the academic year did not significantly alter perceived stress levels, however significantly fewer students did report finding the year "too long". Although FYMS felt ready to work as JDs, they were anxious but not more stressed than the general population about this transition. Attachments that were most valued by FYMS were those that were most closely aligned with the first year JD role.