Background. Online formative assessments have a sound theoretical basis, and are prevalent and popular in higher education settings, but data to establish their educational benefits are lacking. This study attempts to determine whether participation and performance in integrated online formative assessments in the biomedical sciences has measurable effects on learning by junior medical students. Methods. Students enrolled in Phase 1 (Years 1 and 2) of an undergraduate Medicine program were studied over two consecutive years, 2006 and 2007. In seven consecutive courses, end-of-course (EOC) summative examination marks were analysed with respect to the effect of participation and performance in voluntary online formative assessments. Online evaluation surveys were utilized to gather students' perceptions regarding online formative assessments. Results. Students rated online assessments highly on all measures. Participation in formative assessments had a statistically significant positive relationship with EOC marks in all courses. The mean difference in EOC marks for those who participated in formative assessments ranged from 6.3% (95% confidence intervals 1.6 to 11.0; p = 0.009) in Course 5 to 3.2% (0.2 to 6.2; p = 0.037) in Course 2. For all courses, performance in formative assessments correlated significantly with EOC marks (p < 0.001 for each course). The variance in EOC marks that could be explained by performance in the formative assessments ranged from 21.8% in Course 6 to 4.1% in Course 7. Conclusion. The results support the contention that well designed formative assessments can have significant positive effects on learning. There is untapped potential for use of formative assessments to assist learning by medical students and postgraduate medical trainees.