Background Student choice plays a prominent role in the undergraduate curriculum in many contemporary medical schools. A key unanswered question relates to its impact on academic performance. Methods We studied 301 students who were in years 2 and 3 of their medical studies in 2005/06. We investigated the relationship between SSC grade and allocated preference. Separately, we examined the impact of ‘self-proposing’ (students designing and completing their own SSC) on academic performance in other, standard-set, summative assessments throughout the curriculum. The chi-squared test was used to compare academic performance in SSC according to allocated preference. Generalised estimating equations were used to investigate the effect of self-proposing on performance in standard-set examinations. Results (1) Performance in staff-designed SSC was not related to allocated preference. (2) Performance in year 1 main examination was one of the key predictors of performance in written and OSCE examinations in years 2, 3 and 4 (p<0.001). (3) The higher the score in the year 1 examination, the more likely a student was to self-propose in subsequent years (OR [CI] 1.07 [1.03-1.11], p<0.001). (4) Academic performance of students who self-proposed at least once in years 2 and/or 3 varied according to gender and year of course. Conclusion In this study, no association was observed between allocated preference and SSC grade. The effect of self-proposing on academic performance in standard-set examinations was small. Our findings suggest instead that academically brighter students are more likely to design their own modules. Although student choice may have educational benefits, this report does not provide convincing evidence that it improves academic performance.