In Egypt, there is a national concern towards a transition to integrated modern medical educational system. However, the lack of students’ motivation and engagement have been frequently observed and reported. Therefore new strategies should be adopted to improve the quality of education and inspire students and encourage them. This includes implementation of E-learning modality to introduce a variety of teaching materials, to meet the various teaching and learning styles. We aim to report the students’ perception to the newly applied online modality and to compare the level satisfaction of the first three batches. In this retrospective, cross-sectional study, we compared students’ satisfaction regarding the e-Learning tools introduced throughout Phase I. First batch students experienced interactive blended e-Learning, whereas second and third batches received a less interactive e-learning modality. Students’ satisfaction and comments were collected by questionnaires. Results of the feedbacks of the three batches are compared regarding the students’ satisfaction. The mean scores of the rating the blended online modules of the first batch are 4.63±0.69, compared to the second and third batches 1.95± 1.10, and 3.00±1.26 respectively. The entire first batch students agreed that e-Learning is a convenient tool, in contrast to the second and third batches that showed lesser levels of satisfaction owing to the inconsistency of the content. All three batches recommended implementing it regularly and efficiently in all other disciplines.