In this paper the author deals with the use of Petri nets in the e-learning course in the subject Discrete Mathematics taught at the Constantine the Philosopher University in Nitra. Petri nets are used for simulationof students cross through the course. The author describes not only how a student will pass the course but also describes studentscross within one lesson.They present their views through questionnaires. In the questionnaire teachers allocated weight ratio to each thematic unit of Discrete Mathematics syllabus in view of their importance to the subject they teach. On the basis of obtaining feedback it is necessary to propose a suitable methodology of working with the course. It means to review and revise existing e-learning courses. Author assumes that so designed and customized e-learning courses, which are enriched with interactive and multimedia elements will increase the level of students’ knowledge.