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Current changes in social life and economics predetermine transformation processes that are being made in the field of high professional education. Modern society requires specialists ready to develop and implement innovative projects and ideas. Fundamental disciplines, such as chemistry and mathematics are essential for engineering students. E-learning gives us a set of methods and tools that intensify the process of self-development in the educational process. In view of the growing popularity of e-learning as a method of education of modern engineers, the applied educational tool of e-learning has become increasingly important. The paper dwells on the organizing e-learning in natural sciences and mathematics at the higher educational institutions. This article is focused on practical aspects of using learning management system MOODLE in routine teaching practice, especially in independent work of students. It presents pedagogical conditions of effective use of e-courses on the basis of MOODLE for increasing of quality of individual work of students of technical specialties. The method of statistical analysis was employed to show the effectiveness of the electronic courses in the educational process. Research program included means of various psychognosis instruments such as different tests and a diagnostic survey. Most of students said that the e-learning teaching methods improved their knowledge of chemistry and mathematics. More than 88 % of respondents were convinced that e-learning is a necessary complement to the traditional methods of teaching. Statistical analysis by means of a chi-square test showed a markedmarkedmarkedmarked marked tendency towards higher performance on tests by students taught using the web-support of disciplines when compared to the students taught with traditional methods of learning. Improvement of e-learning methods in engineering education has become an important problem.