The article covers the problem of implementation of physical education courses as an elective part of the Federal State Educational Standards for higher education of undergraduate programs. The lesson and the course design for disabled students and students with disabilities are the main focuses of the research article as mastering the course content is obligatory for all students according to the standards of higher education. As the results of the mastering the course, the students are supposed to acquire skills and be competent in implementing activities for physical fitness necessary for personal and professional lifestyle. Though there exists the great amount of theoretical research of the subject under analysis, the practical curriculum design and lesson designs are difficult to implement as they cause a great deal of practical obstacles to overcome: lesson plans to implement in certain environment, lack of specific facilities, the necessity of special medical examinations, grouping students in accordance with their health and fitness level. The research suggests the system of methods, tools and forms of physical education based on various methodological approaches due to the analysis of the state regulative standards, scientific - methodological researches, medical regulations and practical physical education experience in higher education environment. The authors describe the conditions and the model of developing fitness skills and increasing fitness functional state level of disabled students and students with disabilities due to the generalisation of the research. The article suggests various methods of physical education facilities and the principles of their use according to the functional state variations and the diagnosed illnesses of the disabled students. The experience of the implementation of the assessment system of the suggested physical education course for disabled students, including self- assessment techniques is presented, the possible difficulties of the implementation of the course “Elective physical education courses for disabled students and students with disabilities” are studied and analysed. The content of the research article underlines the necessity of work to be done to develop motivation of the students for systematic physical education activities, the necessity to create organisational, scientific- methodological, human resources conditions that may help master the physical fitness skills of the disabled students and students with disabilities as well as increase their physical fitness level. The result of the research may be useful for physical education teachers of various undergraduate degrees in higher education.