The purpose of this study was to identify an appropriate Instructional method for Continuing Medical Education using traditional (lecture based) and two Electronic learning methods. In this quasi-experimental study 90 General physicians and assistants according to the recall of Kermanshah University and by available sampling method in three groups including 30 people participated. The traditional continuing medical education attended in the classroom received lecture based teaching and was taught by experienced college teachers. The E-learning content in the second group was developed by using Microsoft PowerPoint 2010 software with both text and image media and in the third group by using Adobe Flash CS5 software with all five media (text, images, sound, animation and video). It should be noted that the three groups had similar content in terms of text.  The gathering instrument was four questionnaires, included of demographic information (8- items). The rate of learning by comparing pre- test and post-test scores (20- items were written at application level by using the Merrill’s taxonomy) and two questionnaires measuring motivation in learning based on the traditional and e-learning methods (48- items). Data analysis was performed by paired sample T test and chi square, One-way analysis of variance, Kruskal-Wallis and Tukey’s test. The findings showed that there were no significant differences between groups in the average scores achieved in the pre-test exam in three groups (p˂0/05). The results of One-way ANOVA test in the post-test exam showed that the learning rate was not statistically different between Group I and Group II and the third group had the highest rate of increase in learning than the other groups that was statistically significant (p=0.001). Also, participants’ motivation in group II was more than group I and participants using Merrill’s, Reigeluth’s & Keller’s models were more motivated than with the other two methods (p=0.001). Conclusion: As a result, educational method based on instructional and motivational models, in terms of learning and motivation rate to teach physicians, was more effective than traditional teaching methods and merely instructional design models.