The paper deals with a problem (studied by the authors for several years) of the cognitive barriers (difficulties) related to the third component of a peda-gogical triad “how to learn, what to learn, how to study”. At the first stage, methodical approaches to the control of students knowledge in mathematical and natural-science disciplines were worked our. At the next stage, the cognitive barriers of the students arising in the course of studying the above-mentioned disciplines were elucidated. The results obtained during the performance of the two specified stages allowed methodological rec-ommendations related to “The concept of modern natu-ral sciences” discipline to be developed.