Introduction: We aimed to study the role of basic psychological needs and cognitive beliefs on the intrinsic motivation of E-learning students using a causal model. Material and Methods: In this path analysis study we tested the pattern of causal relations through correlation coefficients. The statistical population of the study consisted of all undergraduate students’ (n=218) of the Virtual College of Hadith Sciences in Mashhad during the academic year 2010-2011. The students studied hadith sciences, Quranic teachings and principles of medical ethics. The participants were selected using the convenience sampling method. Data were analyzed using Pearson's correlation coefficient, multiple regression, and path analysis model. SPSS software, version 20 and LSREL (v 8.50) were used for assessing the relationship between the variables. Results: The result of path analysis showed that the model of needs determination (perceived autonomy, perceived competence, perceived relatedness) and intrinsic motivation by cognitive beliefs fits very well (GFI= 0.98, RSMEA=0.05). Conclusion: Paying attention to basic psychological needs increases the students' intrinsic motivation to try and trend towards E-learning. Furthermore, student's cognitive beliefs, such as the quality and applicability of E-learning courses is undeniable in student's motivation and interest.