Instruction, even when designed and based on sound instructional principles, oftentimes does not stimulate learners' motivation to learn. The result may be that learners may not be motivated to pursue lifelong learning and use the knowledge and skills learned to deliver patient care. The purpose of this study was to identify an appropriate integrated instructional design model for Continuing Medical Education using electronic learning method and compare it with traditional method. In this quasi-experimental study 60 General physicians and assistants according to the recall of Kermanshah University of Medical Sciences in Iran and by available sampling method in two 30-staff groups were participated. One group learned through traditional learning method and the other group by e-learning method and by Macromedia flash CS5 software that was based on the integration of instructional and motivational design models; consisting of slides and case studies focusing on the pathogenesis, diagnosis, and clinical management of Acute Respiratory Failure. The data were collected by pretest, posttest, and physicians' motivation questionnaires. There was no significant difference between pretest scores of the two groups (11.37 plus or minus 1.42 VS. 11.73 plus or minus 0.69, P greater than 0.05) but there was significant difference between posttest learning scores (15.2 plus or minus 1.29 VS. 17.53 plus or minus 0.94, p less than 0.05) and motivation of physicians (126.10 plus or minus 3.97 VS. 160.63 plus or minus 22.41, p less than 0.05) in both groups. The physicians' learning and motivation were different in these two instructional methods; therefore, it is recommended that instructional and motivational design be used in future electronic continuing medical education programs. (Contains 3 tables.)