Objective: To determine the frequency and nature of intern underperformance as documented on in-training assessment forms. Methods: A retrospective review of intern assessment forms from a 2 year period (2009-2010) was conducted at a tertiary referral hospital in Brisbane, Queensland. The frequency of interns assessed as 'requiring substantial assistance' and/or 'requires further development' on mid- or end-of-term assessment forms was determined. Forms were analysed by the clinical rotation, time of year and domain(s) of clinical practice in which underperformance was documented. Results: During 2009 and 2010 the overall documented incidence of intern underperformance was 2.4% (95% CI 1.5-3.9%). Clinical rotation in emergency medicine detected significantly more underperformance compared with other rotations (P<0.01). Interns predominantly had difficulty with 'clinical judgment and decision-making skills', 'time management skills' and 'teamwork and colleagues' (62.5%, 55% and 32.5% of underperforming assessments, respectively). Time of the year did not affect frequency of underperformance. A proportion of 13.4% (95% CI 9.2-19.0%) of interns working at the institution over the study period received at least one assessment in which underperformance was documented. Seventy-six per cent of those interns who had underperformance identified by mid-term assessment successfully completed the term following remediation. Conclusion: The prevalence of underperformance among interns is low, although higher than previously suggested. Emergency medicine detects relatively more interns in difficulty than other rotations.