Background In modern medical education, traditional face-to-face teaching is increasingly being supplemented by innovative teaching methods, such as case-based learning or e-learning. Aim of the work Design and evaluation of a new course concept in thoracic surgery to motivate students and at the same time find ways to relieve the medical staff in their teaching activities. Material and methods All students of the third clinical semester at the University of Regensburg completed a case-based course on the topic of pulmonary nodules in the summer semester 2016 and winter semester 2016/2017 as part of the practical course in thoracic surgery. This involved a moderated face-to-face seminar for one group of students and a purely online event for the other group. The knowledge gain and the subjective learning experience of the students were evaluated via questionnaires. Results A total of 190 students took part in the courses, 88 in the face-to-face course and 102 in the online course. Although both groups recorded a significant increase in knowledge as a result of the course intervention, the students in the face-to-face course showed significantly higher subjective satisfaction compared to their peers in the online course. Conclusion Case-based learning was shown to be a promising concept in thoracic surgery education, although establishing online learning procedures proved to be more challenging than presence-based teaching.