BackgroundThis study sought to assess, using subjective (self-assessment) and objective (MCQ) methods, the efficacy of using heart models with ventricular septal defect lesions produced with three-dimensional printing technology in a congenital heart disease curriculum for medical students.MethodsThree computed tomography datasets of three subtypes of ventricular septal defects (perimembranous, subarterial and muscular, one for each) were obtained and processed for building into and printing out 3D models. Then a total of 63 medical students in one class were randomly allocated to two groups (32 students in the experimental, and 31 the control). The two groups participated in a seminar with or without a 3D heart model, respectively. Assessment of this curriculum was carried out using Likert-type questionnaires as well as an objective multiple choice question test assessing both knowledge acquisition, and structural conceptualization. Open-ended questions were also provided for getting advice and suggestion on 3D model utilization in CHD education.ResultsWith these 3D models, feedback shown in the questionnaires from students in experimental group was significantly more positive than their classmates in the control. And the test results also showed a significant difference in structural conceptualization in favor of the experimental group.ConclusionIt is effective to use heart models created using current 3D printing technology for congenital heart disease education. It stimulates students’ interest in congenital heart disease and improves the outcomes of medical education.Electronic supplementary materialThe online version of this article (10.1186/s12909-018-1293-0) contains supplementary material, which is available to authorized users.