Introduction: Two courses on Islamic thoughts are offered at the Iranian higher medical education system to deepen and enhance religious beliefs of Muslim students. Assessing students’ opinion on quality of these courses may improve quality at the higher education system. Therefore, this study aimed to assess students’ opinion on the quality of Islamic course 1 and 2 among students at the Ilam University of Medical Science. Material and Methods: This cross-sectional study was conducted among 296 medical students taking one of the Islamic thought 1 or 2courses during the first semester of academic year 2015-2016. Data were collected using a self-developed questionnaire to assess students’ opinion on three dimensions including content quality, quality of the lecturer as well as planning and effectiveness of the module. We used SPSS version 21 to analyze data using descriptive statistic, t-test and ANOVA. Results: Finding from this study showed that the highest mean score of the quality dimension was 3.42 (SD= 1.05) for content quality followed by 3.23 (SD+ 1.21) for quality of the lecturer and finally 3.16 (SD+ 1.19) for the planning and effectiveness of the module. In addition, the global mean score of the course quality was 3.26 (SD+1.16). There was a significant difference in the mean score of course quality among students from different faculties (p<0.05). Conclusion: Our findings indicated that students perceived the quality of Islamic though courses relatively desirable. However, elaborating different dimensions of quality related to the described courses call for further revision into quality of the lecturer and planning and effectiveness of the module.