Introduction: Part of the postgraduate training in Denmark is theoretical courses organized by the scientific societies. Traditional educational methods like lecturing including questions and answers sections are commonly used. Methods: A traditional 4-days theoretical course was changed into 2-days traditional course and 2 days of self-study. Three self-study modules were developed and included study-guides into the themes of gastroenterology, urology, and electrolytes and water metabolism. Participants had to choose one of the modules and in this module they had to choose one of three possible assignments. The assignments were assessed by two teachers who gave written, specific feedback. The educational effects of course and self-study modules were evaluated using a modified form of Kirkpatrick's 4-level model for evaluating training programs. Results: The composite score for educational effect of the self-study modules compared to traditional course days was higher (P = 0.006). When the effect was split into specific components there was a trend for self-study modules to be superior concerning acquisition of knowledge (P = 0.09), use of knowledge (P = 0.24) and passing on of knowledge (P = 0.09). The trainees spent approximately a mean of 4 days working with the self-study modules and the teacher spent approximately 30 min assessing each assignment. The scores from the assessors correlated well with a Pearson's coefficient of 0.745. Conclusion: The study shows that it is feasible to use evidence based educational methods in planning postgraduate theoretical training and supports existing evidence that didactic programs using predominantly lectures are less effective than interactive and student-centred methods.